Mercurial > repos > artbio > small_rna_map

annotate small_rna_map.r @ 1:2299eb1e7c93 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit d0362e589eb42377b7f10dfcec78be0288220755
author artbio
date Tue, 11 Jul 2017 09:01:19 -0400
parents 1ad5d040f85f
children 7feee0446c5c
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1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
artbio
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1 library(optparse)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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2 library(ggplot2)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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3 library(gridExtra)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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4 library(RColorBrewer)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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5 library(gtable)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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6 library(grid)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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7
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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8 option_list <- list(
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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9 make_option(c("-r", "--output_tab"), type="character", help="path to tabular file"),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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10 make_option("--output_pdf", type = "character", help="path to the pdf file with plot")
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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11 )
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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12
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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13 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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14 args = parse_args(parser)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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15
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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16 theme_set(theme_bw()) #a theme with a white background
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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17 Table = read.delim(args$output_tab, header=T, row.names=NULL)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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18 Table <- within(Table, Nbr_reads[Polarity=="R"] <- (Nbr_reads[Polarity=="R"]*-1))
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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19
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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20 #To assign colors to categorical variables in ggplot2 that have stable mapping
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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21 myColors <- brewer.pal(3,"Set1")
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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22 names(myColors) <- levels(Table$Polarity)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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23 colScale <- scale_colour_manual(name = "Polarity",values = myColors)
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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24
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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25 #Make initial figures
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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26 p <- ggplot(Table, aes(x=Coordinate, y=Nbr_reads, colour=Polarity)) +
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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27 colScale+
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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28 geom_segment(aes(y = 0,
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29 x = Coordinate,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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30 yend = Nbr_reads,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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31 xend = Coordinate,
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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32 color=Polarity),
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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33 alpha=1
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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34 ) +
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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35 geom_segment(aes(y = Nbr_reads,
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36 x = 0,
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37 yend=Nbr_reads,
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38 xend=Chrom_length), alpha=0
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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39 )+
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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40 facet_wrap(Dataset~Chromosome, scales="free", nrow=1, labeller = label_wrap_gen(multi_line = FALSE))+
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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41 scale_y_continuous(breaks = function(x) round(pretty(seq(-(max(x) + 1), (max(x) + 1)))))+#to display only integer values on y axis
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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42 geom_hline(yintercept=0, size=0.3)+
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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43 theme(strip.text = element_text(size = 6, lineheight = 0.1), #specify strip size
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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44 panel.grid.major = element_line(colour = "#ffffff"),#conceal major grid lines
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45 panel.grid.minor = element_line(colour = "#ffffff"),#conceal minor grid lines
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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46 axis.title = element_blank(),# Conceal axis titles
1
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47 axis.text = element_text(size = 6),#modify the size of tick labels along axes
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48 legend.position = "none") # Hide the repeate caption
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49
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50 # Create legend
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51 mylegend <- legendGrob(c("F", "R", "Median", "Mean"), pch=22,
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52 gp=gpar(col = c("red","blue","black","yellow"), fill = c("red","blue","black","yellow")))
0
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53
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54
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55 # The second plot
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56 cols<- c("Median"="#000000", "Mean"="#fffa00")
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57 p2 <- ggplot(Table, aes(x = Coordinate, group=1)) +
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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58 geom_point(aes(y=Median, colour="Median"), alpha=1, size = 1) +
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59 geom_point(aes(y=Mean, colour="Mean"), alpha= 0.3, size = 1.2)+
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60 scale_colour_manual(name="", values=cols)+
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61 expand_limits(y = seq(0,max(Table$Median),by=5)) +
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62 facet_wrap(Dataset~Chromosome, scales="free", nrow=1, labeller = label_wrap_gen(multi_line = FALSE))+
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63 geom_segment(aes(y = Nbr_reads,
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64 x = 0,
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65 yend=Nbr_reads,
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66 xend=Chrom_length), alpha=0
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67 )+
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68 scale_y_continuous(limits = c(0,max(Table$Median)), position = "right")+
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69 theme(strip.text = element_text(size = 6, lineheight = 0.1),
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70 panel.background = element_rect(fill = NA),
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71 panel.grid.major = element_blank(),
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72 panel.grid.minor = element_blank(),
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73 panel.border = element_rect(fill = NA, colour = "grey50"),
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74 axis.text = element_text(size = 6),
1
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75 legend.position = "none"
0
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76 )
1
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77
0
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78 # Transforme ggplot graphs on list of graphs
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79 plot.list1 <- by(data = Table,
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80 INDICES = c(Table$Chromosome),
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81 simplify = TRUE,
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82 FUN = function(x) {
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83 p %+% x
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84 })
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85
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86 plot.list2 <- by(data = Table,
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87 INDICES = c(Table$Chromosome),
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88 simplify = TRUE,
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89 FUN = function(x) {
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90 p2 %+% x
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91 })
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92
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93 # A function to get the original tick mark length
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94 plot_theme <- function(p) {
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95 plyr::defaults(p$theme, theme_get())
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96 }
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97
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98 # ggplot contains many labels that are themselves complex grob;
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99 # usually a text grob surrounded by margins.
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100 # When moving the grobs from, say, the left to the right of a plot,
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101 # Make sure the margins and the justifications are swapped around.
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102 # The function below does the swapping.
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103 # Taken from the cowplot package:
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104 # https://github.com/wilkelab/cowplot/blob/master/R/switch_axis.R
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105
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106 hinvert_title_grob <- function(grob){
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107
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108 # Swap the widths
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109 widths <- grob$widths
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110 grob$widths[1] <- widths[3]
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111 grob$widths[3] <- widths[1]
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112 grob$vp[[1]]$layout$widths[1] <- widths[3]
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113 grob$vp[[1]]$layout$widths[3] <- widths[1]
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114
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115 # Fix the justification
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116 grob$children[[1]]$hjust <- 1 - grob$children[[1]]$hjust
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117 grob$children[[1]]$vjust <- 1 - grob$children[[1]]$vjust
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118 grob$children[[1]]$x <- unit(1, "npc") - grob$children[[1]]$x
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119 grob
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120 }
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121
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122 dual_axis <- function(v1,v2){
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123 # Get the ggplot grobs
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124 g1 <- ggplot_gtable(ggplot_build(v1))
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125 g2 <- ggplot_gtable(ggplot_build(v2))
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126 # Get the locations of the plot panels in g1.
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127 pp <- c(subset(g1$layout, grepl("panel", g1$layout$name), se = t:r))
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128 # Overlap panels for second plot on those of the first plot
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129 g <- gtable_add_grob(g1, g2$grobs[grepl("panel", g1$layout$name)],
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130 pp$t, pp$l, pp$b, pp$l)
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131 # Get the y axis from g2 (axis line, tick marks, and tick mark labels)
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132 index <- which(g2$layout$name == "axis-r-1-1") # Which grob.
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133 yaxis <- g2$grobs[[index]] # Extract the grob
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134 ticks <- yaxis$children[[2]] # swap tick marks and tick mark labels
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135
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136 # Move the tick marks, Tick mark lengths can change.
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137 tml <- plot_theme(p)$axis.ticks.length # Tick mark length
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138 ticks$grobs[[1]]$x <- ticks$grobs[[1]]$x - unit(1, "npc") + tml
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139
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140 # Swap margins and fix justifications for the tick mark labels
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141 ticks$grobs[[2]] <- hinvert_title_grob(ticks$grobs[[2]])
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142
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143 # Put ticks back into yaxis
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144 yaxis$children[[2]] <- ticks
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145
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146 # Put the transformed yaxis on the right side of g1
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147 g <- gtable_add_cols(g, g2$widths[g2$layout[index, ]$l], max(pp$r))
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148 g <- gtable_add_grob(g, yaxis, max(pp$t), max(pp$r) + 1, max(pp$b), max(pp$r) + 1,
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149 clip = "off")
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150
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151 }
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152
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153 plots <- list()
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154 len = length(plot.list1)
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155 for(i in 1:len ) {plots[[i]] <- dual_axis(plot.list1[[i]],plot.list2[[i]])}
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156 # Plotting in multiple pages with different rows
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157 multi.plot<-do.call(marrangeGrob,list(grobs=plots,ncol=1,nrow=8,top=NULL, bottom="Coordinates(nt)", left="Number of reads", right= mylegend))
0
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158 ggsave(args$output_pdf, device="pdf", plot=multi.plot, height=11.69, width=8.2)
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159