Mercurial > repos > iuc > crosscontamination_barcode_filter

annotate scripts/contamination_plot.R @ 1:253c9448f524 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
author iuc
date Mon, 03 Jun 2019 14:55:24 -0400
parents 582b7bd4ae4c
children 5ade5cf200da
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582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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1 #!/usr/bin/env R
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253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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3 suppressPackageStartupMessages(require(ggplot2))
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582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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5 log10histoPlot <- function(title="", columncounts){
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582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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6 #' Log10 histogram plot
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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7 #'
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8 #' @param columncounts colSums(input_matrix)
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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9 #' @param title Title of plot
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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10 #' @return ggplot grob
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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11 dfer <- data.frame(colcounts=log10(columncounts))
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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12 p1 <- ggplot(dfer, aes(x=colcounts)) +
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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13 geom_histogram(binwidth = 0.05, color="black",fill="white") +
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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14 theme(plot.title = element_text(hjust = 0.5)) +
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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15 labs(title=title, y="Frequency", x="Library Size (Log10)")
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17 return(p1)
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18 }
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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20 ## This is calculated by the first call to contaminationPlot
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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21 ## and then re-used by the second call.
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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22 ylim.max = NULL
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582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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24 contaminationPlot <- function(title, columndata, barcode.data, plate.data, RAW)
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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25 {
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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26 coldata = data.frame(colsums=columndata)
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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27 maxval = max(coldata)
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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28 # Set once and once only
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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29 if (is.null(ylim.max)){
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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30 ylim.max <<- maxval + 500
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31 }
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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33 drawPlates <- function(plate.data){ # 0 384 768
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35 plate.boundaries <- plate.data["filtered.plates",]
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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36 if (RAW){
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37 plate.boundaries <- plate.data["unfilter.plates",]
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38 }
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40 plate.minyval <- -200
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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41 plate.color <- "grey"
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42 plate.text.color <- "red"
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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43 plate.text.alpha <- 0.5
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44 plate.height <- 2* maxval / 5
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45 plate.spacing <- 12
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46 plate.height.text <- plate.height - 3000
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47 plate.text.size <- 3
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50 zzz <- lapply(names(plate.boundaries), function(plate.name){
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51 plate.num = as.integer(sub("P","",plate.name))
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52 plate.xval = plate.boundaries[[plate.name]]
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54 ## If not first plate -- inner boundary, print next plate name to the right
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55 if (plate.name != names(plate.boundaries)[length(plate.boundaries)]){
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56 gplot <<- gplot + annotate("text", x=plate.xval + plate.spacing, label=paste("Plate", plate.num + 1),
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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57 size=plate.text.size, y=plate.height*0.7, angle=-90,
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58 color=plate.text.color, alpha=plate.text.alpha)
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59 }
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60 ## If not last plate -- inner boundary, print previous name to the left
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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61 if (plate.name != names(plate.boundaries)[1]){
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62 gplot <<- gplot + annotate("text", x=plate.xval - plate.spacing, label=paste("Plate", plate.num),
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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63 size=plate.text.size, y=plate.height*0.7, angle=90,
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64 color=plate.text.color, alpha=plate.text.alpha)
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65 }
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66 gplot <<- gplot + geom_segment(aes(x=plate.xval, xend=plate.xval, y=plate.minyval, yend=plate.height), color=plate.color, lty=1, size=1)
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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67 })
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68
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69 ## Connecting bar underneath
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70 gplot <<- gplot + geom_segment(aes(x=min(unname(unlist(plate.boundaries))), xend=max(unname(unlist(plate.boundaries))),
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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71 y=plate.minyval, yend=plate.minyval), color=plate.color, lty=1, size=1)
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72 }
0
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73
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74
1
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75 drawBatches <- function(barcode.data, plate.data){
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76 batch.minyval = -200
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77 divide.color <- "grey"
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78 divide.style <- 2 ## dashed
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79 divide.size <- 0.3
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80 boundary.color <- "blue"
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81 boundary.style <- 1
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82 boundary.size <- 0.5
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83 divide.text.true.color <- "blue"
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84 divide.text.false.color <- "black"
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85 divide.text.name.color <- "grey"
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86 batch.text.height <- maxval * 4/5
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87 batch.text.tf.height <- maxval * 2/5
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88 batch.text.tf.spacing <- 12
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89 batch.text.alpha <- 0.8
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90 batch.text.size <- 3
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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91 batch.label.text.size <- 6
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92 batch.height <- maxval * 4/5
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93 divide.height <- maxval * 4/5
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94 batch.spacing <- 24
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95
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96 boundary.pos <- barcode.data["filtered_positions",]
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97 plate.pos <- unname(unlist(plate.data["filtered.plates",])) ## just want values
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98
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99 if (RAW){
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100 boundary.pos <- barcode.data["unfilter_positions",]
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101 divider.pos <- barcode.data["filter_in_unfilter",]
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102 plate.pos <- unname(unlist(plate.data["unfilter.plates",])) ## just want values
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103 }
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104
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105
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106 zzz <- lapply(names(boundary.pos), function(batch.name){
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107 batch.num = as.integer(sub("B","",batch.name))
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108 batch.xval = unname(unlist(boundary.pos[[batch.name]]))
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109
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110 # Plot boundary line only if not intersecting with a plate line
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111 if (!(batch.xval %in% plate.pos)){
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112 gplot <<- gplot + geom_segment(aes(x=batch.xval, xend=batch.xval, y=batch.minyval, yend=batch.height),
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113 color=boundary.color, lty=boundary.style, size=boundary.size)
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114 }
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115
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116 ## Plot labels (except P0)
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117 if (batch.name != "B0"){
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118 if (RAW){
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119 divide.xval = unname(unlist(divider.pos[[batch.name]]))
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120
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121 ## Plot the divider line
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122 gplot <<- gplot + geom_segment(aes(x=divide.xval, xend=divide.xval, y=batch.minyval, yend=divide.height),
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123 color=divide.color, lty=divide.style, size=divide.size)
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124
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125 ## Plot the True/False labels
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126 gplot <<- gplot + annotate("text", x=divide.xval - batch.text.tf.spacing, label="True positives",
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127 size=batch.text.size, y=batch.text.tf.height, angle=+90,
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128 color=divide.text.true.color, alpha=batch.text.alpha)
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129 gplot <<- gplot + annotate("text", x=divide.xval + batch.text.tf.spacing, label="False positives",
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130 size=batch.text.size, y=batch.text.tf.height, angle=-90,
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131 color=divide.text.false.color, alpha=batch.text.alpha)
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132 ## Plot the Batch names
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133 gplot <<- gplot + annotate("text", x=divide.xval, label=batch.name,
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134 size=batch.label.text.size, y=batch.text.height, angle=0,
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135 color = divide.text.name.color, alpha=batch.text.alpha)
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136 } else {
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137 ## Plot the Batch names between blue lines
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138 gplot <<- gplot + annotate("text", x=batch.xval, label=batch.name,
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139 size=batch.label.text.size, y=batch.text.height, angle=0,
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140 color = divide.text.name.color, alpha=batch.text.alpha)
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141 }
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142 }
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143 })
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144 }
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145
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146
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147 plotCells <- function(coldata){
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148 gplot <<- gplot + geom_point(data=coldata, aes(x=1:nrow(coldata), y=coldata$colsums), pch = 16, cex = 1)
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149 }
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150
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151 plotTheme <- function(){
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152 gplot <<- gplot + theme(plot.title = element_text(hjust = 0.5),
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153 axis.ticks.x=element_blank(), axis.ticks.y=element_blank(),
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154 axis.text.x=element_blank()) +
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155 labs(title=paste("Contamination Plot\n", title), y="Library Size", x="Barcode Index") +
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156 coord_cartesian(ylim = c(-200, ylim.max)) +
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157 scale_x_continuous(breaks=NULL)
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158 }
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159
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160
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161 gplot <- ggplot()
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162 drawPlates(plate.data)
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163 drawBatches(barcode.data, plate.data)
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164 plotCells(coldata)
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165 plotTheme()
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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166
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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167 return(gplot)
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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168 }