Mercurial > repos > bgruening > music_deconvolution

annotate scripts/compare.R @ 4:56371b5a2da9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
author bgruening
date Thu, 10 Feb 2022 12:52:31 +0000
parents
children 2ba99a52bd44
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56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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1 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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2 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
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3 suppressWarnings(suppressPackageStartupMessages(library(reshape2)))
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4 suppressWarnings(suppressPackageStartupMessages(library(cowplot)))
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5 ## We use this script to estimate the effectiveness of proportion methods
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7 ## Load Conf
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8 args <- commandArgs(trailingOnly = TRUE)
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9 source(args[1])
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11 method_key <- list("MuSiC" = "est_music",
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12 "NNLS" = "est_nnls")[[est_method]]
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15 scale_yaxes <- function(gplot, value) {
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16 if (is.na(value)) {
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17 gplot
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18 } else {
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19 gplot + scale_y_continuous(lim = c(0, value))
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20 }
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21 }
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24 set_factor_data <- function(bulk_data, factor_name = NULL) {
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25 if (is.null(factor_name)) {
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26 factor_name <- "None" ## change to something plottable
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27 }
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28 pdat <- pData(bulk_data)
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29 sam_fact <- NULL
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30 if (factor_name %in% colnames(pdat)) {
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31 sam_fact <- cbind(rownames(pdat),
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32 as.character(pdat[[factor_name]]))
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33 cat(paste0(" - factor: ", factor_name,
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34 " found in phenotypes\n"))
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35 } else {
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36 ## We assign this as the factor for the entire dataset
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37 sam_fact <- cbind(rownames(pdat),
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38 factor_name)
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39 cat(paste0(" - factor: assigning \"", factor_name,
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40 "\" to whole dataset\n"))
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41 }
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42 colnames(sam_fact) <- c("Samples", "Factors")
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43 return(as.data.frame(sam_fact))
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44 }
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45
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46 ## Due to limiting sizes, we need to load and unload
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47 ## possibly very large datasets.
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48 process_pair <- function(sc_data, bulk_data,
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49 ctypes_label, samples_label, ctypes,
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50 factor_group) {
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51 ## - Generate
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52 est_prop <- music_prop(
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53 bulk.eset = bulk_data, sc.eset = sc_data,
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54 clusters = ctypes_label,
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55 samples = samples_label, select.ct = ctypes, verbose = T)
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56 ## -
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57 estimated_music_props <- est_prop$Est.prop.weighted
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58 estimated_nnls_props <- est_prop$Est.prop.allgene
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59 ## -
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60 fact_data <- set_factor_data(bulk_data, factor_group)
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61 ## -
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62 return(list(est_music = estimated_music_props,
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63 est_nnls = estimated_nnls_props,
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64 bulk_sample_totals = colSums(exprs(bulk_data)),
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65 plot_groups = fact_data))
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66 }
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67
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68 music_on_all <- function(files) {
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69 results <- list()
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70 for (sc_name in names(files)) {
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71 cat(paste0("sc-group:", sc_name, "\n"))
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72 scgroup <- files[[sc_name]]
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73 ## - sc Data
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74 sc_est <- readRDS(scgroup$dataset)
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75 ## - params
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76 celltypes_label <- scgroup$label_cell
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77 samples_label <- scgroup$label_sample
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78 celltypes <- scgroup$celltype
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79
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80 results[[sc_name]] <- list()
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81 for (bulk_name in names(scgroup$bulk)) {
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82 cat(paste0(" - bulk-group:", bulk_name, "\n"))
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83 bulkgroup <- scgroup$bulk[[bulk_name]]
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84 ## - bulk Data
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85 bulk_est <- readRDS(bulkgroup$dataset)
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86 ## - bulk params
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87 pheno_facts <- bulkgroup$pheno_facts
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88 pheno_excl <- bulkgroup$pheno_excl
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89 ##
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90 results[[sc_name]][[bulk_name]] <- process_pair(
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91 sc_est, bulk_est,
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92 celltypes_label, samples_label,
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93 celltypes, bulkgroup$factor_group)
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94 ##
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95 rm(bulk_est) ## unload
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96 }
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97 rm(sc_est) ## unload
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98 }
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99 return(results)
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100 }
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101
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102 plot_all_individual_heatmaps <- function(results) {
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103 pdf(out_heatmulti_pdf, width = 8, height = 8)
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104 for (sc_name in names(results)) {
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105 for (bk_name in names(results[[sc_name]])) {
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106 res <- results[[sc_name]][[bk_name]]
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107 plot_hmap <- Prop_heat_Est(
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108 data.matrix(res[[method_key]]), method.name = est_method) +
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109 ggtitle(paste0("[", est_method, "Cell type ",
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110 "proportions in ",
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111 bk_name, " (Bulk) based on ",
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112 sc_name, " (scRNA)")) +
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113 xlab("Cell Types (scRNA)") +
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114 ylab("Samples (Bulk)") +
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115 theme(axis.text.x = element_text(angle = -90),
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116 axis.text.y = element_text(size = 6))
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117 print(plot_hmap)
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118 }
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119 }
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120 dev.off()
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121 }
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122
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123 merge_factors_spread <- function(grudat_spread, factor_groups) {
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124 ## Generated
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125 merge_it <- function(matr, plot_groups, valname) {
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126 ren <- melt(lapply(matr, function(mat) {
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127 mat["ct"] <- rownames(mat); return(mat)}))
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128 ## - Grab factors and merge into list
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129 ren_new <- merge(ren, plot_groups, by.x = "variable", by.y = "Samples")
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130 colnames(ren_new) <- c("Sample", "Cell", valname, "Bulk", "Factors")
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131 return(ren_new)
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132 }
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133 tab <- merge(merge_it(grudat$spread$prop, factor_groups, "value.prop"),
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134 merge_it(grudat$spread$scale, factor_groups, "value.scale"),
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135 by = c("Sample", "Cell", "Bulk", "Factors"))
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136 return(tab)
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137 }
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138
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139
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140 plot_grouped_heatmaps <- function(results) {
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141 pdf(out_heatmulti_pdf, width = 8, height = 8)
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142 for (sc_name in names(results)) {
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143 named_list <- sapply(
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144 names(results[[sc_name]]),
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145 function(n) {
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146 ## We transpose the data here, because
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147 ## the plotting function omits by default
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148 ## the Y-axis which are the samples.
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149 ## Since the celltypes are the common factor
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150 ## these should be the Y-axis instead.
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151 t(data.matrix(results[[sc_name]][[n]][[method_key]]))
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152 }, simplify = F, USE.NAMES = T)
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153 named_methods <- names(results[[sc_name]])
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154 ##
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155 plot_hmap <- Prop_heat_Est(
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156 named_list,
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157 method.name = named_methods) +
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158 ggtitle(paste0("[", est_method, "] Cell type ",
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159 "proportions of ",
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160 "Bulk Datasets based on ",
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161 sc_name, " (scRNA)")) +
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162 xlab("Samples (Bulk)") +
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163 ylab("Cell Types (scRNA)") +
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164 theme(axis.text.x = element_text(angle = -90),
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165 axis.text.y = element_text(size = 6))
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166 print(plot_hmap)
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167 }
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168 dev.off()
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169 }
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170
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171 ## Desired plots
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172 ## 1. Pie chart:
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173 ## - Per Bulk dataset (using just normalised proportions)
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174 ## - Per Bulk dataset (multiplying proportions by nreads)
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175
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176 unlist_names <- function(results, method, prepend_bkname=FALSE) {
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177 unique(sort(
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178 unlist(lapply(names(results), function(scname) {
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179 lapply(names(results[[scname]]), function(bkname) {
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180 res <- get(method)(results[[scname]][[bkname]][[method_key]])
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181 if (prepend_bkname) {
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182 ## We *do not* assume unique bulk sample names
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183 ## across different bulk datasets.
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184 res <- paste0(bkname, "::", res)
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185 }
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186 return(res)
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187 })
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188 }))
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189 ))
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190 }
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191
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192 summarized_matrix <- function(results) { # nolint
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193 ## We assume that cell types MUST be unique, but that sample
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194 ## names do not need to be. For this reason, we must prepend
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195 ## the bulk dataset name to the individual sample names.
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196 all_celltypes <- unlist_names(results, "colnames")
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197 all_samples <- unlist_names(results, "rownames", prepend_bkname = TRUE)
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198
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199 ## Iterate through all possible samples and populate a table.
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200 ddff <- data.frame()
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201 ddff_scale <- data.frame()
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202 for (cell in all_celltypes) {
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203 for (sample in all_samples) {
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204 group_sname <- unlist(strsplit(sample, split = "::"))
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205 bulk <- group_sname[1]
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206 id_sample <- group_sname[2]
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207 for (scgroup in names(results)) {
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208 if (bulk %in% names(results[[scgroup]])) {
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209 mat_prop <- results[[scgroup]][[bulk]][[method_key]]
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210 vec_counts <- results[[scgroup]][[bulk]]$bulk_sample_totals
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211 ## - We use sample instead of id_sample because we need to
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212 ## extract bulk sets from the complete matrix later. It's
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213 ## messy, yes.
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214 if (cell %in% colnames(mat_prop)) {
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215 ddff[cell, sample] <- mat_prop[id_sample, cell]
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216 ddff_scale[cell, sample] <- mat_prop[id_sample, cell] * vec_counts[[id_sample]] #nolint
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217 } else {
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218 ddff[cell, sample] <- 0
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219 ddff_scale[cell, sample] <- 0
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220 }
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221 }
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222 }
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223 }
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224 }
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225 return(list(prop = ddff, scaled = ddff_scale))
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226 }
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227
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228 flatten_factor_list <- function(results) {
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229 ## Get a 2d DF of all factors across all bulk samples.
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230 res <- c()
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231 for (scgroup in names(results)) {
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232 for (bulkgroup in names(results[[scgroup]])) {
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233 dat <- results[[scgroup]][[bulkgroup]]$plot_groups
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234 dat$Samples <- paste0(bulkgroup, "::", dat$Samples) #nolint
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235 res <- rbind(res, dat)
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236 }
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237 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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238 return(res)
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239 }
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240
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241 group_by_dataset <- function(summat) {
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242 bulk_names <- unlist(
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243 lapply(names(files), function(x) names(files[[x]]$bulk)))
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244 mat_names <- colnames(summat$prop)
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245 bd <- list()
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246 bd_scale <- list()
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247 bd_spread_scale <- list()
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248 bd_spread_prop <- list()
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249 for (bname in bulk_names) {
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250 subs <- mat_names[startsWith(mat_names, paste0(bname, "::"))]
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251 ## -
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252 bd[[bname]] <- rowSums(summat$prop[, subs])
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253 bd_scale[[bname]] <- rowSums(summat$scaled[, subs])
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254 bd_spread_scale[[bname]] <- summat$scaled[, subs]
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255 bd_spread_prop[[bname]] <- summat$prop[, subs]
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256 }
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257 return(list(prop = as.data.frame(bd),
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258 scaled = as.data.frame(bd_scale),
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259 spread = list(scale = bd_spread_scale,
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260 prop = bd_spread_prop)))
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261 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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262
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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263 summarize_heatmaps <- function(grudat_spread_melt, do_factors) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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264 ## -
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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265 do_single <- function(grudat_melted, yaxis, xaxis, fillval, title,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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266 ylabs = element_blank(), xlabs = element_blank(),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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267 use_log = TRUE, size = 11) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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268 ## Convert from matrix to long format
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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269 melted <- grudat_melted ## copy?
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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270 if (use_log) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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271 melted[[fillval]] <- log10(melted[[fillval]] + 1)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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272 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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273 return(ggplot(melted) +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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274 geom_tile(aes_string(y = yaxis, x = xaxis, fill = fillval),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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275 colour = "white") +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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276 scale_fill_gradient2(low = "steelblue", high = "red",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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277 mid = "white", name = element_blank()) +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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278 theme(axis.text.x = element_text(angle = -90, hjust = 0,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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279 size = size)) +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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280 ggtitle(label = title) + xlab(xlabs) + ylab(ylabs))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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281 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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282
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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283 do_gridplot <- function(title, xvar, plot="both", ncol=2, size = 11) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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284 do_logged <- (plot %in% c("log", "both"))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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285 do_normal <- (plot %in% c("normal", "both"))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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286 plist <- list()
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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287 if (do_logged) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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288 plist[["1"]] <- do_single(grudat_spread_melt, "Cell", xvar,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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289 "value.scale", "Reads (log10+1)",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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290 size = size)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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291 plist[["2"]] <- do_single(grudat_spread_melt, "Cell", xvar,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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292 "value.prop", "Sample (log10+1)",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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293 size = size)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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294 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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295 if (do_normal) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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296 plist[["A"]] <- do_single(grudat_spread_melt, "Cell", xvar,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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297 "value.scale", "Reads", use_log = F,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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298 size = size)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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299 plist[["B"]] <- do_single(grudat_spread_melt, "Cell", xvar,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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300 "value.prop", "Sample", use_log = F,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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301 size = size)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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302 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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303 return(plot_grid(ggdraw() + draw_label(title, fontface = "bold"),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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304 plot_grid(plotlist = plist, ncol = ncol),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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305 ncol = 1, rel_heights = c(0.05, 0.95)))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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306
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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307 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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308 p1 <- do_gridplot("Cell Types vs Bulk Datasets", "Bulk", "both", )
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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309 p2a <- do_gridplot("Cell Types vs Samples", "Sample", "normal", 1,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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310 size = 8)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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311 p2b <- do_gridplot("Cell Types vs Samples (log10+1)", "Sample", "log", 1,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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312 size = 8)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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313 p3 <- ggplot + theme_void()
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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314 if (do_factors) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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315 p3 <- do_gridplot("Cell Types against Factors", "Factors", "both")
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316 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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317 return(list(bulk = p1,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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318 samples = list(log = p2b, normal = p2a),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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319 factors = p3))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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320 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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321
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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322 summarize_boxplots <- function(grudat_spread, do_factors) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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323 common1 <- ggplot(grudat_spread, aes(x = value.prop)) + ggtitle("Sample") +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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324 xlab(element_blank()) + ylab(element_blank())
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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325 common2 <- ggplot(grudat_spread, aes(x = value.scale)) + ggtitle("Reads") +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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326 xlab(element_blank()) + ylab(element_blank())
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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327
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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328 A <- B <- list() #nolint
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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329 ## Cell type by sample
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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330 A$p1 <- common2 + geom_boxplot(aes(y = Cell, color = Bulk))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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331 A$p2 <- common1 + geom_boxplot(aes(y = Cell, color = Bulk))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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332 ## Sample by Cell type
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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333 B$p1 <- common2 + geom_boxplot(aes(y = Bulk, color = Cell)) +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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334 ylab("Bulk Dataset")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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335 B$p2 <- common1 + geom_boxplot(aes(y = Bulk, color = Cell)) +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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336 ylab("Bulk Dataset")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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337 ## -- Factor plots are optional
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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338 A$p3 <- B$p3 <- A$p4 <- B$p4 <- ggplot() + theme_void()
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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339
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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340 if (do_factors) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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341 A$p3 <- common1 + geom_boxplot(aes(y = Cell, color = Factors))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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342 A$p4 <- common2 + geom_boxplot(aes(y = Cell, color = Factors))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
343 B$p3 <- common1 + geom_boxplot(aes(y = Bulk, color = Factors)) +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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344 ylab("Bulk Dataset")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
345 B$p4 <- common2 + geom_boxplot(aes(y = Bulk, color = Factors)) +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
346 ylab("Bulk Dataset")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
347 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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348
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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349 title_a <- "Cell Types against Bulk"
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
350 title_b <- "Bulk Datasets against Cells"
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
351 if (do_factors) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
352 title_a <- paste0(title_a, " and Factors")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
353 title_b <- paste0(title_b, " and Factors")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
354 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
355
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
356 a_all <- plot_grid(ggdraw() + draw_label(title_a, fontface = "bold"),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
357 plot_grid(plotlist = A, ncol = 2),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
358 ncol = 1, rel_heights = c(0.05, 0.95))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
359 b_all <- plot_grid(ggdraw() + draw_label(title_b, fontface = "bold"),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
360 plot_grid(plotlist = B, ncol = 2),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
361 ncol = 1, rel_heights = c(0.05, 0.95))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
362 return(list(cell = a_all, bulk = b_all))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
363 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
364
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
365 filter_output <- function(grudat_spread_melt, out_filt) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
366 print_red <- function(comment, red_list) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
367 cat(paste(comment, paste(red_list, collapse = ", "), "\n"))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
368 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
369 grudat_filt <- grudat_spread_melt
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
370 print_red("Total Cell types:", unique(grudat_filt$Cell))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
371 if (!is.null(out_filt$cells)) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
372 grudat_filt <- grudat_filt[grudat_filt$Cell %in% out_filt$cells, ]
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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373 print_red(" - selecting:", out_filt$cells)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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374 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
375 print_red("Total Factors:", unique(grudat_spread_melt$Factors))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
376 if (!is.null(out_filt$facts)) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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377 grudat_filt <- grudat_filt[grudat_filt$Factors %in% out_filt$facts, ]
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
378 print_red(" - selecting:", out_filt$facts)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
379 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
380 return(grudat_filt)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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381 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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382
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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383
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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384 results <- music_on_all(files)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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385
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
386 if (heat_grouped_p) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
387 plot_grouped_heatmaps(results)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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388 } else {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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389 plot_all_individual_heatmaps(results)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
390 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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391
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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392 save.image("/tmp/sesh.rds")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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393
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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394 summat <- summarized_matrix(results)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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395 grudat <- group_by_dataset(summat)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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396 grudat_spread_melt <- merge_factors_spread(grudat$spread,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
397 flatten_factor_list(results))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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398
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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399
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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400
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
401 ## The output filters ONLY apply to boxplots, since these take
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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402 do_factors <- (length(unique(grudat_spread_melt[["Factors"]])) > 1)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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403
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
404 grudat_spread_melt_filt <- filter_output(grudat_spread_melt, out_filt)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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405
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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406 heat_maps <- summarize_heatmaps(grudat_spread_melt_filt, do_factors)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
407 box_plots <- summarize_boxplots(grudat_spread_melt_filt, do_factors)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
408
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
409 pdf(out_heatsumm_pdf, width = 14, height = 14)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
410 print(heat_maps)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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parents:
diff changeset
411 print(box_plots)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
412 dev.off()
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
413
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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414 ## Generate output tables
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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415 stats_prop <- lapply(grudat$spread$prop, function(x) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
416 t(apply(x, 1, summary))})
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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417 stats_scale <- lapply(grudat$spread$scale, function(x) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
418 t(apply(x, 1, summary))})
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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419
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
420 writable2 <- function(obj, prefix, title) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
421 write.table(obj,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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422 file = paste0("report_data/", prefix, "_",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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423 title, ".tabular"),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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424 quote = F, sep = "\t", col.names = NA)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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425 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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diff changeset
426 ## Make the value table printable
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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427 grudat_spread_melt$value.scale <- as.integer(grudat_spread_melt$value.scale) # nolint
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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428 colnames(grudat_spread_melt) <- c("Sample", "Cell", "Bulk", "Factors",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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429 "CT Prop in Sample", "Number of Reads")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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430
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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431 writable2(grudat_spread_melt, "values", "Data Table")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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432 writable2(summat$prop, "values", "Matrix of Cell Type Sample Proportions")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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433 writable2({
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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434 aa <- as.matrix(summat$scaled); mode(aa) <- "integer"; aa
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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435 }, "values", "Matrix of Cell Type Read Counts")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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436
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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437 for (bname in names(stats_prop)) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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438 writable2(stats_prop[[bname]], "stats", paste0(bname, ": Sample Props"))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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439 writable2(stats_scale[[bname]], "stats", paste0(bname, ": Read Props"))
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
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440 }