Mercurial > repos > artbio > gsc_high_dimensions_visualisation

annotate high_dim_visu.R @ 0:241dd93219d7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
author artbio
date Thu, 11 Jul 2019 12:31:00 -0400
parents
children 8e6ce12edd90
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0
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
1 # load packages that are provided in the conda env
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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2 options( show.error.messages=F,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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3 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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4 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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5 requiredPackages = c('optparse', 'Rtsne', 'ggplot2', 'ggfortify')
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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6 warnings()
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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7 library(optparse)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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8 library(FactoMineR)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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9 library(factoextra)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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10 library(Rtsne)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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11 library(ggplot2)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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12 library(ggfortify)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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13 library(RColorBrewer)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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14 library(ClusterR)
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15
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16 # Arguments
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17 option_list = list(
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18 make_option(
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19 "--data",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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20 default = NA,
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21 type = 'character',
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22 help = "Input file that contains expression value to visualise"
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23 ),
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24 make_option(
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25 "--sep",
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26 default = '\t',
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27 type = 'character',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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28 help = "File separator [default : '%default' ]"
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29 ),
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30 make_option(
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31 "--colnames",
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32 default = TRUE,
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33 type = 'logical',
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34 help = "Consider first line as header ? [default : '%default' ]"
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35 ),
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36 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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37 "--out",
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38 default = "res.tab",
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39 type = 'character',
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40 help = "Output name [default : '%default' ]"
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41 ),
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42 make_option(
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43 "--labels",
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44 default = FALSE,
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45 type = 'logical',
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46 help = "add labels in scatter plots [default : '%default' ]"
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47 ),
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48 make_option(
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49 "--factor",
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50 default = '',
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51 type = 'character',
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52 help = "A two column table that specifies factor levels for contrasting data [default : '%default' ]"
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53 ),
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54 make_option(
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55 "--visu_choice",
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56 default = 'PCA',
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57 type = 'character',
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58 help = "visualisation method ('PCA', 'tSNE', 'HCPC') [default : '%default' ]"
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59 ),
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60 make_option(
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61 "--table_coordinates",
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62 default = '',
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63 type = 'character',
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64 help = "Table with plot coordinates [default : '%default' ]"
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65 ),
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66 make_option(
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67 "--Rtsne_seed",
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68 default = 42,
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69 type = 'integer',
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70 help = "Seed value for reproducibility [default : '%default' ]"
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71 ),
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72 make_option(
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73 "--Rtsne_dims",
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74 default = 2,
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75 type = 'integer',
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76 help = "Output dimensionality [default : '%default' ]"
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77 ),
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78 make_option(
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79 "--Rtsne_initial_dims",
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80 default = 50,
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81 type = 'integer',
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82 help = "The number of dimensions that should be retained in the initial PCA step [default : '%default' ]"
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83 ),
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84 make_option(
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85 "--Rtsne_perplexity",
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86 default = 5.0,
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87 type = 'numeric',
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diff changeset
88 help = "perplexity [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
89 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
90 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
91 "--Rtsne_theta",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
92 default = 1.0,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
93 type = 'numeric',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
94 help = "theta [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
95 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
96 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
97 "--Rtsne_max_iter",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
98 default = 1000,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
99 type = 'integer',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
100 help = "max_iter [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
101 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
102 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
103 "--Rtsne_pca",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
104 default = TRUE,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
105 type = 'logical',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
106 help = "Whether an initial PCA step should be performed [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
107 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
108 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
109 "--Rtsne_pca_center",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
110 default = TRUE,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
111 type = 'logical',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
112 help = "Should data be centered before pca is applied? [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
113 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
114 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
115 "--Rtsne_pca_scale",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
116 default = FALSE,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
117 type = 'logical',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
118 help = "Should data be scaled before pca is applied? [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
119 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
120 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
121 "--Rtsne_normalize",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
122 default = TRUE,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
123 type = 'logical',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
124 help = "Should data be normalized internally prior to distance calculations? [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
125 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
126 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
127 "--Rtsne_exaggeration_factor",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
128 default = 12.0,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
129 type = 'numeric',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
130 help = " Exaggeration factor used to multiply the P matrix in the first part of the optimization [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
131 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
132 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
133 "--PCA_npc",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
134 default = 5,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
135 type = 'integer',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
136 help = "number of dimensions kept in the results [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
137 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
138 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
139 "--PCA_x_axis",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
140 default = 1,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
141 type = 'integer',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
142 help = "PC to plot in the x axis [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
143 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
144 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
145 "--PCA_y_axis",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
146 default = 2,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
147 type = 'integer',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
148 help = "PC to plot in the y axis [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
149 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
150 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
151 "--HCPC_ncluster",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
152 default = -1,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
153 type = 'numeric',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
154 help = "nb.clust, number of clusters to consider in the hierarchical clustering. [default : -1 let HCPC to optimize the number]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
155 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
156 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
157 "--HCPC_npc",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
158 default = 5,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
159 type = 'integer',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
160 help = "npc, number of dimensions which are kept for HCPC analysis [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
161 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
162 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
163 "--HCPC_metric",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
164 default = 'euclidian',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
165 type = 'character',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
166 help = "Metric to be used for calculating dissimilarities between observations, available 'euclidian' or 'manhattan' [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
167 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
168 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
169 "--HCPC_method",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
170 default = 'ward',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
171 type = 'character',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
172 help = "Clustering method between 'ward','average','single', 'complete', 'weighted' [default :'%default']"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
173 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
174 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
175 "--pdf_out",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
176 default = "out.pdf",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
177 type = 'character',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
178 help = "pdf of plots [default : '%default' ]"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
179 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
180 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
181 "--HCPC_consol",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
182 default = 'TRUE',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
183 type = 'logical',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
184 help = "If TRUE, a k-means consolidation is performed [default :'%default']"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
185 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
186 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
187 "--HCPC_itermax",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
188 default = '10',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
189 type = 'integer',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
190 help = "The maximum number of iterations for the consolidation [default :'%default']"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
191 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
192 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
193 "--HCPC_min",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
194 default = '3',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
195 type = 'integer',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
196 help = "The least possible number of clusters suggested [default :'%default']"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
197 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
198 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
199 "--HCPC_max",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
200 default = -1,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
201 type = 'integer',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
202 help = "The higher possible number of clusters suggested [default :'%default']"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
203 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
204 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
205 "--HCPC_clusterCA",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
206 default = 'rows',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
207 type = 'character',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
208 help = "A string equals to 'rows' or 'columns' for the clustering of Correspondence Analysis results [default :'%default']"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
209 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
210 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
211 "--HCPC_kk",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
212 default = -1,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
213 type = 'numeric',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
214 help = "The maximum number of iterations for the consolidation [default :'%default']"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
215 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
216 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
217 "--HCPC_clust",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
218 default = "",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
219 type = 'character',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
220 help = "Output result of HCPC clustering : two column table (cell identifiers and clusters) [default :'%default']"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
221 ),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
222 make_option(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
223 "--mutual_info",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
224 default = "",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
225 type = "character",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
226 help = "Output file of external validation of HCPC clustering with factor levels [default :'%default']"
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
227 )
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
228 )
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
229
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
230 opt = parse_args(OptionParser(option_list = option_list),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
231 args = commandArgs(trailingOnly = TRUE))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
232
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
233 if (opt$sep == "tab") {opt$sep <- "\t"}
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
234 if (opt$sep == "comma") {opt$sep <- ","}
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
235 if(opt$HCPC_max == -1) {opt$HCPC_max <- NULL}
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
236 if(opt$HCPC_kk == -1) {opt$HCPC_kk <- Inf}
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
237
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
238 ##Add legend to plot()
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
239 legend.col <- function(col, lev){
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
240
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
241 opar <- par
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
242
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
243 n <- length(col)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
244
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
245 bx <- par("usr")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
246
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
247 box.cx <- c(bx[2] + (bx[2] - bx[1]) / 1000,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
248 bx[2] + (bx[2] - bx[1]) / 1000 + (bx[2] - bx[1]) / 50)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
249 box.cy <- c(bx[3], bx[3])
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
250 box.sy <- (bx[4] - bx[3]) / n
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
251
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
252 xx <- rep(box.cx, each = 2)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
253
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
254 par(xpd = TRUE)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
255 for(i in 1:n){
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
256
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
257 yy <- c(box.cy[1] + (box.sy * (i - 1)),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
258 box.cy[1] + (box.sy * (i)),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
259 box.cy[1] + (box.sy * (i)),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
260 box.cy[1] + (box.sy * (i - 1)))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
261 polygon(xx, yy, col = col[i], border = col[i])
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
262
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
263 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
264 par(new = TRUE)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
265 plot(0, 0, type = "n",
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266 ylim = c(min(lev), max(lev)),
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267 yaxt = "n", ylab = "",
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268 xaxt = "n", xlab = "",
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269 frame.plot = FALSE)
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artbio
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270 axis(side = 4, las = 2, tick = FALSE, line = .25)
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271 par <- opar
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272 }
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273
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274
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275 data = read.table(
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276 opt$data,
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277 check.names = FALSE,
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artbio
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278 header = opt$colnames,
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279 row.names = 1,
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280 sep = opt$sep
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281 )
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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282
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artbio
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283 # Contrasting factor and its colors
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284 if (opt$factor != '') {
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285 contrasting_factor <- read.delim(
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artbio
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286 opt$factor,
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artbio
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287 header = TRUE
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288 )
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artbio
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289 rownames(contrasting_factor) <- contrasting_factor[,1]
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artbio
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290 contrasting_factor <- contrasting_factor[colnames(data),]
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artbio
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291 colnames(contrasting_factor) <- c("id","factor")
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292 if(is.numeric(contrasting_factor$factor)){
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artbio
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293 factor_cols <- rev(brewer.pal(n = 11, name = "RdYlGn"))[contrasting_factor$factor]
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294 } else {
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295 contrasting_factor$factor <- as.factor(contrasting_factor$factor)
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296 if(nlevels(contrasting_factor$factor) == 2){
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297 colors_labels <- c("#E41A1C", "#377EB8")
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298 } else {
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299 colors_labels <- brewer.pal(nlevels(contrasting_factor$factor), name = 'Paired')
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300 }
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301 factorColors <-
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artbio
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302 with(contrasting_factor,
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artbio
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303 data.frame(factor = levels(contrasting_factor$factor),
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304 color = I(colors_labels)
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305 )
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artbio
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306 )
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artbio
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307 factor_cols <- factorColors$color[match(contrasting_factor$factor,
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artbio
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308 factorColors$factor)]
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309 }
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diff changeset
310 } else {
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artbio
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311 factor_cols <- rep("deepskyblue4", length(rownames(data)))
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312 }
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313
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314 ################ t-SNE ####################
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315 if (opt$visu_choice == 'tSNE') {
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artbio
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316 # filter and transpose df for tsne and pca
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317 tdf = t(data)
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318 # make tsne and plot results
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319 set.seed(opt$Rtsne_seed) ## Sets seed for reproducibility
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320
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artbio
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321 tsne_out <- Rtsne(tdf,
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artbio
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diff changeset
322 dims = opt$Rtsne_dims,
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artbio
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diff changeset
323 initial_dims = opt$Rtsne_initial_dims,
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artbio
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324 perplexity = opt$Rtsne_perplexity ,
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artbio
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325 theta = opt$Rtsne_theta,
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326 max_iter = opt$Rtsne_max_iter,
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327 pca = opt$Rtsne_pca,
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artbio
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328 pca_center = opt$Rtsne_pca_center,
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artbio
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329 pca_scale = opt$Rtsne_pca_scale,
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diff changeset
330 normalize = opt$Rtsne_normalize,
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artbio
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diff changeset
331 exaggeration_factor=opt$Rtsne_exaggeration_factor)
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332
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diff changeset
333 embedding <- as.data.frame(tsne_out$Y[,1:2])
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diff changeset
334 embedding$Class <- as.factor(rownames(tdf))
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artbio
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335 gg_legend = theme(legend.position="right")
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artbio
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diff changeset
336 if (opt$factor == '') {
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artbio
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diff changeset
337 ggplot(embedding, aes(x=V1, y=V2)) +
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artbio
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diff changeset
338 geom_point(size=1, color='deepskyblue4') +
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artbio
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339 gg_legend +
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artbio
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340 xlab("t-SNE 1") +
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artbio
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341 ylab("t-SNE 2") +
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artbio
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342 ggtitle('t-SNE') +
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artbio
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343 if (opt$labels) {
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diff changeset
344 geom_text(aes(label=Class),hjust=-0.2, vjust=-0.5, size=1.5, color='deepskyblue4')
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345 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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346 } else {
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artbio
parents:
diff changeset
347 if(is.numeric(contrasting_factor$factor)){
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
348 embedding$factor <- contrasting_factor$factor
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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349 } else {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
350 embedding$factor <- as.factor(contrasting_factor$factor)
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351 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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diff changeset
352
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
353 ggplot(embedding, aes(x=V1, y=V2, color=factor)) +
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
354 geom_point(size=1) + #, color=factor_cols
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
355 gg_legend +
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
356 xlab("t-SNE 1") +
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
357 ylab("t-SNE 2") +
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
358 ggtitle('t-SNE') +
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
359 if (opt$labels) {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
360 geom_text(aes(label=Class, colour=factor),hjust=-0.2, vjust=-0.5, size=1.5)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
361 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
362 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
363 ggsave(file=opt$pdf_out, device="pdf")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
364
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
365 #save coordinates table
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
366 if(opt$table_coordinates != ''){
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
367 coord_table <- cbind(rownames(tdf), round(as.data.frame(tsne_out$Y), 6))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
368 colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$Rtsne_dims)))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
369 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
370 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
371
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
372
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
373 ######### make PCA with FactoMineR #################
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
374 if (opt$visu_choice == 'PCA') {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
375 pca <- PCA(t(data), ncp=opt$PCA_npc, graph=FALSE)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
376 pdf(opt$pdf_out)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
377 if (opt$labels == FALSE) {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
378 plot(pca, axes = c(opt$PCA_x_axis,opt$PCA_y_axis), label="none" , col.ind = factor_cols)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
379 } else {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
380 plot(pca, axes = c(opt$PCA_x_axis,opt$PCA_y_axis), cex=0.2 , col.ind = factor_cols)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
381 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
382 if (opt$factor != '') {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
383 if(is.factor(contrasting_factor$factor)) {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
384 legend(x = 'topright',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
385 legend = as.character(factorColors$factor),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
386 col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
387 } else {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
388 legend.col(col = rev(brewer.pal(n = 11, name = "RdYlGn")), lev = cut(contrasting_factor$factor, 11, label = FALSE))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
389 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
390 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
391 dev.off()
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
392
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
393 #save coordinates table
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
394 if(opt$table_coordinates != ''){
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
395 coord_table <- cbind(rownames(pca$ind$coord), round(as.data.frame(pca$ind$coord), 6))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
396 colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$PCA_npc)))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
397 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
398
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
399 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
400
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
401 ########### make HCPC with FactoMineR ##########
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
402 if (opt$visu_choice == 'HCPC') {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
403
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
404 # HCPC starts with a PCA
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
405 pca <- PCA(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
406 t(data),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
407 ncp = opt$HCPC_npc,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
408 graph = FALSE,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
409 )
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
410
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
411 PCA_IndCoord = as.data.frame(pca$ind$coord) # coordinates of observations in PCA
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
412
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
413 # Hierarchical Clustering On Principal Components Followed By Kmean Clustering
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
414 res.hcpc <- HCPC(pca,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
415 nb.clust=opt$HCPC_ncluster, metric=opt$HCPC_metric, method=opt$HCPC_method,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
416 graph=F,consol=opt$HCPC_consol,iter.max=opt$HCPC_itermax,min=opt$HCPC_min,max=opt$HCPC_max,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
417 cluster.CA=opt$HCPC_clusterCA,kk=opt$HCPC_kk)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
418 # HCPC plots
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
419 dims <- head(as.data.frame(res.hcpc$call$t$res$eig),2) # dims variances in column 2
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
420 pdf(opt$pdf_out)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
421 plot(res.hcpc, choice="tree")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
422 plot(res.hcpc, choice="bar")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
423 plot(res.hcpc, choice="3D.map")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
424 if (opt$labels == FALSE) {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
425 plot(res.hcpc, choice="map", label="none")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
426 } else {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
427 plot(res.hcpc, choice="map")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
428 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
429
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
430 # user contrasts on the pca
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
431 if (opt$factor != '') {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
432 plot(pca, label="none", col.ind = factor_cols)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
433 if(is.factor(contrasting_factor$factor)) {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
434 legend(x = 'topright',
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
435 legend = as.character(factorColors$factor),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
436 col = factorColors$color, pch = 16, bty = 'n', xjust = 1, cex=0.7)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
437
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
438 ## Normalized Mutual Information
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
439 sink(opt$mutual_info)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
440 res <- external_validation(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
441 true_labels = as.numeric(contrasting_factor$factor),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
442 clusters = as.numeric(res.hcpc$data.clust$clust),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
443 summary_stats = TRUE
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
444 )
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
445 sink()
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
446
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
447 } else {
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
448 legend.col(col = rev(brewer.pal(n = 11, name = "RdYlGn")), lev = cut(contrasting_factor$factor, 11, label = FALSE))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
449 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
450 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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451 ## Clusters to which individual observations belong # used ?
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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452 # Clust <- data.frame(Cluster = res.hcpc$data.clust[, (nrow(data) + 1)],
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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453 # Observation = rownames(res.hcpc$data.clust))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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454 # metadata <- data.frame(Observation=colnames(data), row.names=colnames(data))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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455 # metadata = merge(y = metadata,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
456 # x = Clust,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
457 # by = "Observation")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
458
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
459 # unclear utility
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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460 # ObsNumberPerCluster = as.data.frame(table(metadata$Cluster))
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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461 # colnames(ObsNumberPerCluster) = c("Cluster", "ObsNumber")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
462 #
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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463 # ## Silhouette Plot # not used
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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464 # hc.cut = hcut(PCA_IndCoord,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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465 # k = nlevels(metadata$Cluster),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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466 # hc_method = "ward.D2")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
467 #
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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468 # Sil = fviz_silhouette(hc.cut)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
469 # sil1 = as.data.frame(Sil$data)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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470
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
471 dev.off()
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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472
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
473 if(opt$table_coordinates != ''){
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
474 coord_table <- cbind(Cell=rownames(res.hcpc$call$X),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
475 round(as.data.frame(res.hcpc$call$X[, -length(res.hcpc$call$X)]), 6),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
476 as.data.frame(res.hcpc$call$X[, length(res.hcpc$call$X)])
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
477 )
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
478 colnames(coord_table)=c("Cells",paste0("DIM",(1:opt$HCPC_npc)),"Cluster")
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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479 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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480
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
481 if(opt$HCPC_clust != ""){
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
482 res_clustering <- data.frame(Cell = rownames(res.hcpc$data.clust),
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
483 Cluster = res.hcpc$data.clust$clust)
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
diff changeset
484
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
485 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
486
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
487 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
488
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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diff changeset
489 ## Return coordinates file to user
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
diff changeset
490
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
491 if(opt$table_coordinates != ''){
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
492 write.table(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
493 coord_table,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
494 file = opt$table_coordinates,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
495 sep = "\t",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
496 quote = F,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
497 col.names = T,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff changeset
498 row.names = F
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
499 )
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
500 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
501
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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502
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
503 if(opt$HCPC_clust != ""){
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
504 write.table(
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
505 res_clustering,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
506 file = opt$HCPC_clust,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
507 sep = "\t",
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
508 quote = F,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
509 col.names = T,
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
510 row.names = F
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
511 )
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
diff changeset
512 }
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
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513
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
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514
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
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515
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
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516
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
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517
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
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518
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
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519
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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520
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parents:
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521
241dd93219d7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
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parents:
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522
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artbio
parents:
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523