Mercurial > repos > azomics > flowsom_cross_comp

annotate FlowSOMMApIndividualFCS.R @ 2:f611ded6c6df draft default tip

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planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
author azomics
date Fri, 29 Sep 2023 07:20:00 +0000
parents a1054bd1060a
children
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rev   line source
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e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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1 #!/usr/bin/Rscript
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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2 # Module for Galaxy
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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3 # Generates FlowSOM reference tree
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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4 # with FlowSOM AggregateFlowFrames
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5 ######################################################################
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6 # Copyright (c) 2017 Northrop Grumman.
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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7 # All rights reserved.
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8 ######################################################################
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9 #
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10 # Version 1
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11 # Cristel Thomas
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12 #
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13 #
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14 library(FlowSOM)
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15 library(flowCore)
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16
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17 ## geometric mean from
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18 # https://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in
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19 gm_mean <- function(x, na_rm = TRUE) {
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20 exp(sum(log(x[x > 0]), na.rm = na_rm) / length(x))
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21 }
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22
1
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23 pretty_marker_names <- function(flow_frame) {
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24 n <- flow_frame@parameters@data[, "name"]
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25 d <- flow_frame@parameters@data[, "desc"]
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26 d[is.na(d)] <- n[is.na(d)]
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27 pretty_names <- list()
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28 if (any(grepl("#", d))) {
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29 # Support for hashtag notation:
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30 pretty_names <- gsub("#(.*)$", " (\\1)", d)
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31 } else {
1
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32 pretty_names <- paste(d, " <", n, ">", sep = "")
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33 }
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34 return(pretty_names)
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35 }
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36
1
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37 check_markers <- function(fcsfiles, flag_ff = FALSE) {
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38 marker_check <- TRUE
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39 for (i in seq_along(fcsfiles)) {
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40 if (flag_ff) {
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41 fcs <- readRDS(fcsfiles[i])
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42 } else {
1
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43 fcs <- read.FCS(fcsfiles[i], transformation = FALSE)
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44 }
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45 if (i == 1) {
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46 m1 <- as.vector(pData(parameters(fcs))$desc)
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47 } else {
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48 m2 <- as.vector(pData(parameters(fcs))$desc)
1
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49 if (is.na(all(m1 == m2))) {
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50 mm1 <- is.na(m1)
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51 mm2 <- is.na(m2)
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52 if (all(mm1 == mm2)) {
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53 if (!all(m1 == m2, na.rm = TRUE)) {
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54 marker_check <- FALSE
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55 }
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56 } else {
1
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57 marker_check <- FALSE
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58 }
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59 } else if (!all(m1 == m2)) {
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60 marker_check <- FALSE
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61 }
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62 }
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63 }
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64 if (!marker_check) {
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65 quit(save = "no", status = 13, runLast = FALSE)
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66 }
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67 }
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68
1
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69 map_to_tree <- function(filenames, filepaths,
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70 flag_ff = FALSE, reftree, cluster = 10,
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71 outdir = "", flag_meta = FALSE,
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72 mfi = "mfi", stat1 = "", stat2 = "",
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73 stat3 = "", plot = "", mplot = "") {
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74
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75 check_markers(filepaths, flag_ff)
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76 # get tree
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77 fst <- readRDS(reftree)
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78 plots <- FALSE
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79 mplots <- FALSE
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80 dir.create(outdir)
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81 if (!plot == "") {
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82 dir.create(plot)
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83 plots <- TRUE
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84 }
1
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85 if (!mplot == "") {
0
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86 dir.create(mplot)
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87 mplots <- TRUE
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88 }
1
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89 meta_c <- metaClustering_consensus(fst$map$codes, k = cluster, seed = 33)
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90 nb_pop <- if (flag_meta) cluster else max(fst$map$mapping[, 1])
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91 nb_samples <- length(filepaths)
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92 nb_marker <- length(fst$prettyColnames)
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93 print_markers <- gsub(" <.*>", "", fst$prettyColnames)
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94 print_markers_ff <- append(print_markers, "Population")
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95
1
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96 m_stat1 <- matrix(0, nrow = nb_samples, ncol = (nb_pop + 2))
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97 colnames(m_stat1) <- c("FileID", "SampleName", seq_len(nb_pop))
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98
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99 sink(stat2)
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100 cat(print_markers, sep = "\t")
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101 cat("\tPercentage\tPopulation\tSampleName\n")
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102 sink()
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103
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104 col_m3 <- c("Population")
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105 for (m in print_markers){
1
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106 m1 <- paste(m, "mean", sep = "_")
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107 m2 <- paste(m, "median", sep = "_")
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108 m3 <- paste(m, "stdev", sep = "_")
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109 col_m3 <- append(col_m3, c(m1, m2, m3))
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110 }
1
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111 col_stat3 <- c(col_m3,
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112 "Percentage_mean",
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113 "Percentage_median",
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114 "Percentage_stdev")
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115
1
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116 for (i in seq_along(filepaths)) {
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117 if (flag_ff) {
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118 ff <- readRDS(filepaths[i])
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119 } else {
1
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120 ff <- read.FCS(filepaths[i], transformation = FALSE)
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121 }
1
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122 if (i == 1) {
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123 # compare to tree markers
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124 pm <- pretty_marker_names(ff)
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125 if (!all(fst$prettyColnames %in% pm)) {
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126 quit(save = "no", status = 14, runLast = FALSE)
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127 }
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128 }
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129
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130 fsom <- NewData(fst, ff)
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131
1
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132 if (mplots) {
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133 markers <- colnames(ff)
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134 tmpmplot <- paste(filenames[i], "marker_plots.pdf", sep = "_")
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135 pdf(file.path(mplot, tmpmplot), useDingbats = FALSE, onefile = TRUE)
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136 for (marker in markers){
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137 PlotMarker(fsom, marker)
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138 }
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139 dev.off()
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140 }
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141
1
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142 if (!plot == "") {
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143 plotpath <- paste(filenames[i], "tree.png", sep = "_")
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144 png(file.path(plot, plotpath), type = "cairo", height = 800, width = 800)
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145 PlotStars(fsom, backgroundValues = as.factor(meta_c))
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146 dev.off()
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147 }
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148
1
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149 m <- matrix(0, nrow = nrow(ff), ncol = 1)
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150 s <- seq_len(nrow(ff))
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151 if (flag_meta) {
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152 m[s, ] <- meta_c[fsom$map$mapping[, 1]]
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153 } else {
1
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154 m[s, ] <- fsom$map$mapping[, 1]
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155 }
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156 colnames(m) <- "FlowSOM"
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157 ff <- cbind2(ff, m)
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158 out <- exprs(ff)
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159 colnames(out) <- print_markers_ff
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160
1
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161 clr_table <- paste(filenames[i], "clustered.flowclr", sep = "_")
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162 write.table(out,
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163 file = file.path(outdir, clr_table),
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164 quote = FALSE,
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165 row.names = FALSE,
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166 col.names = TRUE,
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167 sep = "\t",
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168 append = FALSE)
0
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169
1
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170 cluster_count <- table(out[, "Population"])
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171 cluster_prop <- prop.table(cluster_count) * 100
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172 m1_tmp <- numeric(nb_pop)
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173 for (j in 1:nb_pop){
1
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174 if (as.character(j) %in% names(cluster_count)) {
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175 m1_tmp[[j]] <- format(
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176 round(cluster_prop[[as.character(j)]], 2),
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177 nsmall = 2)
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178 }
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179 }
1
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180 samplename <- paste("Sample", i, sep = "")
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181 m_stat1[i, ] <- c(filenames[i], samplename, m1_tmp)
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182 # flowstat2
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183 # Marker1 Marker2 Marker3 ... Population Percentage SampleName
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184 # MFIs for each marker
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185 # dimension ==> col = nb of markers + 3; row = nb of files * nb of clusters
1
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186 if (mfi == "mfi") {
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187 m2 <- aggregate(out[, 1:nb_marker], list(out[, nb_marker + 1]), mean)
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188 } else if (mfi == "mdfi") {
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189 m2 <- aggregate(out[, 1:nb_marker], list(out[, nb_marker + 1]), median)
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190 } else {
1
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191 m2 <- aggregate(out[, 1:nb_marker], list(out[, nb_marker + 1]), gm_mean)
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192 }
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193
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194 m2["Percentage"] <- as.character(cluster_prop)
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195 m2["Population"] <- as.character(m2$Group.1)
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196 m2["SampleName"] <- samplename
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197 m2t <- as.matrix(m2[2:length(m2)])
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198 write.table(m2t,
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199 file = stat2,
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200 quote = FALSE,
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201 row.names = FALSE,
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202 col.names = FALSE,
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203 sep = "\t",
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204 append = TRUE)
0
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205
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206 }
1
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207 write.table(m_stat1,
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208 file = stat1,
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209 quote = FALSE,
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210 row.names = FALSE,
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211 col.names = TRUE,
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212 sep = "\t",
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213 append = FALSE)
0
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214
1
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215 m2df <- read.table(stat2, sep = "\t", header = TRUE)
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216 ag <- aggregate(m2df[, 0:nb_marker + 1],
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217 list(m2df[, nb_marker + 2]),
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218 function(x) c(mn = mean(x), med = median(x), stdv = sd(x)))
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219 m3t <- as.matrix(ag)
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220 colnames(m3t) <- col_stat3
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221 write.table(m3t, file = stat3,
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222 quote = FALSE,
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223 row.names = FALSE,
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224 col.names = TRUE, sep = "\t",
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225 append = FALSE)
0
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226 }
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227
1
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228 flow_frame_or_fcs <- function(filenames,
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229 filepaths,
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230 reftree,
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231 cluster = 10, outdir = "",
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232 flag_meta = FALSE,
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233 mfi = "mfi", stat1 = "", stat2 = "",
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234 stat3 = "", plot = "", mplot = "") {
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235 is_fcs <- FALSE
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236 is_ff <- FALSE
0
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237 flag_ff <- FALSE
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238 i <- 0
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239 for (f in filepaths){
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240 tryCatch({
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241 is_fcs <- isFCSfile(f)
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242 }, error = function(ex) {
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243 print(paste(ex))
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244 })
1
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245 if (!is_fcs) {
0
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246 tryCatch({
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247 ff <- readRDS(f)
1
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248 is_ff <- TRUE
0
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249 }, error = function(ex) {
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250 print(paste(ex))
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251 })
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252 } else {
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253 i <- i + 1
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254 }
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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255 if (!is_ff && !is_fcs) {
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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256 quit(save = "no", status = 10, runLast = FALSE)
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257 }
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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258 }
1
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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259 if (i == 0) {
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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260 flag_ff <- TRUE
1
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261 } else if (!i == length(filenames)) {
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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262 quit(save = "no", status = 12, runLast = FALSE)
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263 }
1
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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264 map_to_tree(filenames,
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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265 filepaths,
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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266 flag_ff, reftree, cluster, outdir, flag_meta,
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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267 mfi, stat1, stat2, stat3, plot, mplot)
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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268 }
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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269
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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270 args <- commandArgs(trailingOnly = TRUE)
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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271 plot <- ""
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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272 mplot <- ""
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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273 m <- 8
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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274 flag_meta <- FALSE
1
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275 if (args[4] == "meta") {
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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276 flag_meta <- TRUE
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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277 }
1
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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278 if (args[9] == "newDataTrees") {
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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279 plot <- "newDataTrees"
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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280 m <- m + 1
1
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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281 if (args[10] == "newDataMarkers") {
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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282 mplot <- "newDataMarkers"
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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283 m <- m + 1
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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284 }
1
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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285 } else if (args[9] == "newDataMarkers") {
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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286 mplot <- "newDataMarkers"
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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287 m <- m + 1
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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288 }
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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289
1
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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290 n <- m + 1
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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291 nb_files <- (length(args) - m) / 2
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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292 files1 <- character(nb_files)
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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293 files2 <- character(nb_files)
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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294 j <- 1
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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295 file_list <- args[n:length(args)]
1
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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296 for (i in seq_along(file_list)) {
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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297 if (i %% 2) {
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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298 files1[[j]] <- file_list[i]
1
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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299 files2[[j]] <- file_list[i + 1]
0
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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300 j <- j + 1
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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301 }
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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302 }
e796ed5dfd02 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit 2f04d23cb47d9b233d159c54ff406e56c87746e0"
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303
1
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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diff changeset
304 flow_frame_or_fcs(files2,
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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diff changeset
305 files1, args[1], as.numeric(args[3]), args[2], flag_meta,
a1054bd1060a planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_cross_comp commit f2ed3cfcc71ccf61cf6058533d217443318fd024
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diff changeset
306 args[5], args[6], args[7], args[8], plot, mplot)