Mercurial > repos > blankenberglab > gpca

annotate r-gpca.R @ 4:ceaa4d404115 draft default tip

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planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 9ad682131963a72c88a5af1cfc99f90ea9d42a08
author blankenberglab
date Mon, 03 Dec 2018 15:07:32 -0500
parents 8def7dda3bee
children
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0
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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1 #!/usr/bin/env Rscript
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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2 library(optparse)
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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3 library(gPCA)
1
d93629e79f5e planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 3b791d44853d8928046914cd93112bdcf89d4965
blankenberglab
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4 options(bitmapType='cairo')
0
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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5
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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6 # parse options
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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7 option_list = list(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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8 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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9 c("--version"),
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blankenberglab
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10 action = "store_true",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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11 default = FALSE,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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12 help = "Print version and exit"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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13 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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14 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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15 c("-i", "--batch"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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16 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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17 default = NA,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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18 type = 'character',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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19 help = "Input batch"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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20 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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21 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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22 c("-d", "--data"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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23 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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24 default = NA,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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25 type = 'character',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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26 help = "Input data"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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27 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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28 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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29 c("-n", "--nperm"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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30 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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31 default = 1000,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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32 type = 'numeric',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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33 help = "Number of permutations to preform"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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34 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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35 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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36 c("-c", "--center"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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37 action = "store_true",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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38 default = FALSE,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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39 help = "Is the input batch and data centered [default %default]"
3
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40 ),
0
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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41 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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42 c("-y", "--scaleY"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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43 action = "store_true",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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44 default = FALSE,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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45 help = "Scale to Y axis"
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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46 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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47 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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48 c("-f", "--filt"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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49 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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50 default = NULL,
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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51 type = 'numeric',
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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52 help = "Retain features"
3
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53 ),
0
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54 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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55 c( "--npcs"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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56 action = "store",
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blankenberglab
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57 default = 3,
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blankenberglab
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58 type = 'numeric',
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blankenberglab
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59 help = "Number of principal components to plot"
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60 ),
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61 make_option(
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62 c("-p", "--path"),
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63 action = "store",
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64 default = '$html_outfile.extra_files_path',
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65 type = 'character',
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66 help = "File path"
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67 ),
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68 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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69 c("-s", "--seed"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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70 action = "store",
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71 default = NULL,
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72 type = 'numeric',
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73 help = "Set a seed number"
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74 ),
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blankenberglab
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75 make_option(
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76 c("-x", "--numbers_outfile"),
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blankenberglab
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77 action = "store",
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78 default = NA,
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79 type = 'character',
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80 help = "Numbers output"
3
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81 ),
0
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82 make_option(
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83 c("-o", "--html_outfile"),
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84 action = "store",
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85 default = NA,
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86 type = 'character',
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87 help = "Output",
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88 )
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89 )
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90
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91 opt <-parse_args(OptionParser(option_list = option_list))
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92
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93 if (opt$version){
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94 # print version and exit
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95 cat(paste("gPCA version", toString(packageVersion("gPCA"))), "\n")
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96 quit()
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97 }
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98
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99 # Check parameter values
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100 if ( ! file.exists(opt$batch)){
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101 stop((paste('File for batch', opt$batch, 'does not exist')))
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102 }
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103 if ( ! file.exists(opt$data)){
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104 stop((paste('File for data', opt$data, 'does not exist')))
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105 }
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106
1
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107 dir.create(opt$path);
0
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108 data<-t(as.matrix(read.delim(opt$data, row.names=1, header=TRUE, sep="\t")))
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109 batch<-as.matrix(read.delim(opt$batch, header=TRUE, row.names=1, sep="\t"))
0
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110
1
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111 write('#Batch\tDelta\tP-value\tCumulative Variance',file = opt$numbers_outfile, append=TRUE)
3
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112 write('<!DOCTYPE html>
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113 <html lang="en">
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114 <head>
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115 <style>
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116 table, td, th {
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117 margin-left:auto;
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118 margin-right:auto;
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119 border: 2px solid black;
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120 }
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121 h2, ul {
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122 text-align:left;
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123 }
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124 h1 {
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125 text-align:center;
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126 }
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127 body {
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128 text-align: center;
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129 }
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130 p {
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131 font-size: 0px;
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132 }
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133 </style>
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134 <title>HTML gPCA</title></head><body><p>If you are seeing this then CSS is not whitelisted</p><h2 id = "top">Table of Contents</h2><ul>', file = opt$html_outfile, append=TRUE)
1
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135
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136 for (row in 1:nrow(batch)) {
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137 write(paste0('<li><a href="#',row.names(batch)[row],'">',row.names(batch)[row],'</a></li>'), file=opt$html_outfile, append=TRUE)
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138 }
3
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139 write('</ul>', file=opt$html_outfile, append=TRUE)
1
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140 for (row in 1:nrow(batch)) {
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141 batch1<-as.numeric(factor(batch[row,]))
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142 out<-gPCA.batchdetect(x=data, batch=batch1, center=opt$center, scaleY=opt$scaleY, nperm=opt$nperm, filt=opt$filt, seed=opt$seed)
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143 out$varPCg1<-((out$varPCg1-out$varPCu1)/out$varPCg1)*100
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144 write(paste(row.names(batch)[row],out$delta,out$p.val,out$varPCg1,sep="\t"),file = opt$numbers_outfile, append=TRUE)
0
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145
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146 # General Distribution
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147 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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148 png(paste(opt$path,'/gDist_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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149 gDist(out)
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150 invisible(dev.off())
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151
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152 # Guided/Unguided 1v2
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153 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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154 png(paste(opt$path,'/guided_1v2_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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155 PCplot(out,ug="unguided",type="1v2")
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156 invisible(dev.off())
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157 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
1
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158 png(paste(opt$path,'/unguided_1v2_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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159 PCplot(out,ug="unguided",type="1v2")
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160 invisible(dev.off())
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161
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162 # Guided/Unguided comp,3
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163 par(mai=c(0.65,0.65,0.1,0.1),cex=0.8)
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164 png(paste(opt$path,'/guided_npcs_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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165 PCplot(out,ug="guided",type="comp",npcs=opt$npcs)
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166 invisible(dev.off())
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167 par(mai=c(0.65,0.65,0.1,0.1),cex=0.8)
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168 png(paste(opt$path,'/unguided_npcs_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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169 PCplot(out,ug="unguided",type="comp",npcs=opt$npcs)
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170 invisible(dev.off())
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171
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172 # Guided/Unguided CumlativeVarPlot
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173 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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174 png(paste(opt$path,'/guided_var_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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175 CumulativeVarPlot(out,ug="guided",col="blue")
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176 invisible(dev.off())
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177 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
1
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178 png(paste(opt$path,'/unguided_var_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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179 CumulativeVarPlot(out,ug="unguided",col="blue")
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180 invisible(dev.off())
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181
1
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182 write(paste0('
3
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183 <h1 id="',row.names(batch)[row],'">',row.names(batch)[row],'</h1>
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184 <br>
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185 <table>
0
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186 <tr>
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187 <th>Delta</th><th>P-value</th><th>varPCg1</th>
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188 </tr>
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189 <tr>
3
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190 <td>',out$delta,'&nbsp;</td><td>',out$p.val,'&nbsp;</td><td>',out$varPCg1,'</td>
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191 </tr>
3
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192 </table><br>
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193 <h3>gDist</h3><br><img src="gDist_',row,'.png" alt="gDist"/>
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194 <br>
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195 <h3>Guided 1v2</h3><br><img src="guided_1v2_',row,'.png" alt="guided_1v2" /><br>
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196 <h3>Unguided 1v2</h3><br><img src="unguided_1v2_',row,'.png" alt="unguided_1v2" /><br>
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197 <h3>Guided Compare to ',opt$npcs,'</h3><br><img src="guided_npcs_',row,'.png" alt="guided_npcs"/><br>
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198 <h3>Unguided Compare to ',opt$npcs,'</h3><br><img src="unguided_npcs_',row,'.png" alt="unguided_npcs"/><br>
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199 <h3>Guided Cumulative Variance</h3><br><img src="guided_var_',row,'.png" alt="guided_var" /><br>
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200 <h3>Unguided Cumulative Variance</h3><br><img src="unguided_var_',row,'.png" alt="unguided_var" /><br>
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201 '), file = opt$html_outfile, append=TRUE)
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202 }
3
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203 write(paste('<a href="#top">Back to Top</a></body></html>'),file = opt$html_outfile, append=TRUE)