Mercurial > repos > iuc > phyloseq_plot_richness

annotate phyloseq_plot_bar.R @ 8:d6cbeb48294d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d6888da7aba38b97f6cb827355f2de436565684a
author iuc
date Tue, 04 Feb 2025 14:39:26 +0000
parents 4faa9c663b38
children 10a7732528b2
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1a6c2cc92c6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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1 #!/usr/bin/env Rscript
1a6c2cc92c6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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2
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3 # Load libraries
1a6c2cc92c6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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4 suppressPackageStartupMessages(library("optparse"))
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5 suppressPackageStartupMessages(library("phyloseq"))
1a6c2cc92c6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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6 suppressPackageStartupMessages(library("ggplot2"))
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7
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8 # Define options
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9 option_list <- list(
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10 make_option(c("--input"),
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11 action = "store", dest = "input",
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12 help = "Input file containing a phyloseq object"
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13 ),
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14 make_option(c("--x"),
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15 action = "store", dest = "x",
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16 help = "Variable for x-axis (e.g., 'Sample', 'Phylum')"
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17 ),
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18 make_option(c("--fill"),
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19 action = "store", dest = "fill", default = NULL,
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20 help = "Variable for fill color (e.g., 'Genus', 'Order') (optional)"
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21 ),
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22 make_option(c("--facet"),
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23 action = "store", dest = "facet", default = NULL,
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24 help = "Facet by variable (optional)"
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25 ),
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26 make_option(c("--output"),
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27 action = "store", dest = "output",
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28 help = "Output file (PDF)"
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29 ),
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30 make_option(c("--topX"),
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31 action = "store", dest = "topX", default = NULL,
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32 help = "Show only the top X taxa based on abundance (e.g., '10') (optional)"
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33 ),
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34 make_option(c("--keepOthers"),
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35 action = "store_true", dest = "keepOthers", default = FALSE,
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36 help = "Keep taxa not in topX and label them as 'Others' (optional)"
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37 ),
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38 make_option(c("--keepNonAssigned"),
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39 action = "store_true", dest = "keepNonAssigned", default = FALSE,
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40 help = "Keep taxa labeled as 'Not Assigned' (optional)"
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41 ),
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42 make_option(c("--normalize"),
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43 action = "store_true", dest = "normalize", default = FALSE,
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44 help = "Normalize abundances to sum to 100% (optional)"
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45 ),
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46 make_option(c("--width"),
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47 action = "store", dest = "width", default = 10,
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48 type = "numeric", help = "Width of the output plot in inches"
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49 ),
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50 make_option(c("--height"),
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51 action = "store", dest = "height", default = 8,
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52 type = "numeric", help = "Height of the output plot in inches"
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53 ),
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54 make_option(c("--device"),
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55 action = "store", dest = "device", default = "pdf",
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56 help = "Output format (e.g., 'pdf', 'png', 'jpeg')"
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57 ),
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58 make_option(c("--nolines"),
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59 type = "logical", default = FALSE,
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60 help = "Remove borders (lines) around bars (TRUE/FALSE)"
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61 )
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62 )
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63
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64 # Parse arguments
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65 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
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66 args <- parse_args(parser, positional_arguments = TRUE)
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67 opt <- args$options
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68
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69 # Validate required options
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70 if (is.null(opt$input) || opt$input == "") {
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71 stop("Error: Input file is required.")
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72 }
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73 if (is.null(opt$output) || opt$output == "") {
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74 stop("Error: Output file is required.")
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75 }
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76
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77 # Load phyloseq object
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78 print(paste("Trying to read:", opt$input))
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79 physeq <- readRDS(opt$input)
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80
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81 # Normalize to relative abundances if requested
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82 if (opt$normalize) {
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83 print("Normalizing abundances to sum to 100%...")
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84 physeq <- transform_sample_counts(physeq, function(x) 100 * x / sum(x))
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85 }
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86
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87 # Debug: Check available taxonomic ranks
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88 print("Available taxonomic ranks:")
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89 print(colnames(tax_table(physeq)))
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90
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91 # Handle missing or unassigned taxa for all ranks
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92 if (opt$keepNonAssigned) {
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93 # Replace NA or empty values with 'Not Assigned' for all ranks
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94 tax_ranks <- colnames(tax_table(physeq))
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95
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96 for (rank in tax_ranks) {
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97 if (rank %in% colnames(tax_table(physeq))) {
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98 # replace NA or empty values with 'Not Assigned'
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99 tax_table(physeq)[, rank][is.na(tax_table(physeq)[, rank])] <- "Not Assigned"
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100 }
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101 }
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102 }
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103
8
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104 # Filter to top X taxa if requested
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105 if (!is.null(opt$topX) && opt$topX != "") {
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106 topX <- as.numeric(opt$topX)
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107 if (is.na(topX) || topX <= 0) {
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108 stop("Error: topX should be a positive number.")
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109 }
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110
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111 tax_rank <- opt$fill
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112 if (!tax_rank %in% colnames(tax_table(physeq))) {
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113 stop(paste("Error: Tax rank", tax_rank, "not found in tax_table."))
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114 }
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115
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116 physeq_agg <- tax_glom(physeq, taxrank = tax_rank)
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117 taxa_abundance <- taxa_sums(physeq_agg)
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118 tax_table_agg <- tax_table(physeq_agg)
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119 taxa_abundance_by_rank <- tapply(taxa_abundance, tax_table_agg[, tax_rank], sum)
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120 top_taxa <- names(sort(taxa_abundance_by_rank, decreasing = TRUE))[1:topX]
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121
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122 print("Top taxa:")
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123 print(top_taxa)
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124
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125 otus_in_top_taxa <- rownames(tax_table_agg)[tax_table_agg[, tax_rank] %in% top_taxa]
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126
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127 if (opt$keepOthers) {
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128 tax_table(physeq_agg)[, tax_rank][!rownames(tax_table_agg) %in% otus_in_top_taxa] <- "Others"
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129 physeq <- physeq_agg
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130 } else {
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131 physeq <- prune_taxa(otus_in_top_taxa, physeq_agg)
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132 }
3
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133 }
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134
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135 # Generate bar plot
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136 if (!is.null(opt$x) && opt$x != "") {
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137 p <- plot_bar(physeq, x = opt$x, fill = opt$fill) +
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138 geom_bar(aes(fill = !!sym(opt$fill)),
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139 stat = "identity", position = "stack",
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140 color = ifelse(opt$nolines, NA, "black")
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141 )
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142 } else {
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143 p <- plot_bar(physeq, fill = opt$fill) +
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144 geom_bar(aes(fill = !!sym(opt$fill)),
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145 stat = "identity", position = "stack",
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146 color = ifelse(opt$nolines, NA, "black")
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147 )
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148 }
3
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149
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150 # Optional: Add faceting if specified
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151 if (!is.null(opt$facet) && opt$facet != "") {
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152 sample_vars <- colnames(sample_data(physeq))
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153 if (opt$facet %in% sample_vars) {
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154 p <- p + facet_wrap(as.formula(paste("~", opt$facet)))
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155 } else {
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156 warning(paste("Facet variable", opt$facet, "not found in sample data. Skipping faceting."))
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157 }
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158 }
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159
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160 # Save to output file
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161 ggsave(
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162 filename = opt$output,
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163 plot = p,
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164 width = opt$width,
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165 height = opt$height,
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166 device = opt$device
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167 )