Mercurial > repos > iuc > phyloseq_plot_richness

annotate phyloseq_plot_bar.R @ 7:4faa9c663b38 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 53ece29ec3f7e3c2c51d0ff9849e6193863cca71
author iuc
date Sat, 25 Jan 2025 17:12:03 +0000
parents a20bc31f2821
children d6cbeb48294d
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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
1a6c2cc92c6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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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"))
1a6c2cc92c6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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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(
1a6c2cc92c6e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
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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"),
a20bc31f2821 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 26f87cc62468c9c329b33246af4f14e2659856f9
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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')"
3
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57 )
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58 )
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59
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60 # Parse arguments
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61 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
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62 args <- parse_args(parser, positional_arguments = TRUE)
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63 opt <- args$options
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64
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65 # Validate required options
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66 if (is.null(opt$input) || opt$input == "") {
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67 stop("Error: Input file is required.")
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68 }
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69 if (is.null(opt$output) || opt$output == "") {
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70 stop("Error: Output file is required.")
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71 }
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72
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73 # Load phyloseq object
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74 print(paste("Trying to read:", opt$input))
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75 physeq <- readRDS(opt$input)
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76
6
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77 # Normalize to relative abundances if requested
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78 if (opt$normalize) {
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79 print("Normalizing abundances to sum to 100%...")
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80 physeq <- transform_sample_counts(physeq, function(x) 100 * x / sum(x))
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81 }
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82
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83 if (opt$keepNonAssigned) {
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84 # Add synthetic "Not Assigned" for missing/NA taxa
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85 tax_table(physeq) <- apply(tax_table(physeq), c(1, 2), function(x) ifelse(is.na(x) | x == "", "Not Assigned", x))
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86 }
3
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87 # Check if the 'x' and 'fill' variables are valid
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88 sample_vars <- colnames(sample_data(physeq))
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89
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90 # If topX is provided, filter the phyloseq object to show only top X taxa
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91 if (!is.null(opt$topX) && opt$topX != "") {
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92 topX <- as.numeric(opt$topX)
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93 if (is.na(topX) || topX <= 0) {
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94 stop("Error: topX should be a positive number.")
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95 }
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96
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97 # Aggregate the data at the selected rank (e.g., Phylum)
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98 tax_rank <- opt$fill # Adjust as necessary
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99 physeq_agg <- tax_glom(physeq, taxrank = tax_rank)
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100
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101 # Get the abundance of each taxon at the selected rank
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102 taxa_abundance <- taxa_sums(physeq_agg)
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103
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104 # Summarize the abundance at each taxonomic rank (grouping by taxonomic name)
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105 tax_table_agg <- tax_table(physeq_agg)
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106 taxa_abundance_by_rank <- tapply(taxa_abundance, tax_table_agg[, tax_rank], sum)
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107
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108 # Identify the top X taxa by summed abundance
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109 top_taxa <- names(sort(taxa_abundance_by_rank, decreasing = TRUE))[1:topX]
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110
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111 print("Only plotting taxa in TopX taxa group:")
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112 print(top_taxa)
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113
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114 # Get the OTUs corresponding to the top taxa
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115 otus_in_top_taxa <- rownames(tax_table_agg)[tax_table_agg[, tax_rank] %in% top_taxa]
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116
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117 if (opt$keepOthers) {
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118 # Label taxa not in top_taxa as "Others"
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119 tax_table(physeq_agg)[, tax_rank][!rownames(tax_table(physeq_agg)) %in% otus_in_top_taxa] <- "Others"
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120 physeq <- physeq_agg
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121 } else {
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122 # Subset the phyloseq object to keep only the top X taxa
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123 physeq_filtered <- prune_taxa(otus_in_top_taxa, physeq_agg)
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124 physeq <- physeq_filtered
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125 }
3
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126 }
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127
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128 # Generate bar plot
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129 if (!is.null(opt$x) && opt$x != "") {
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130 p <- plot_bar(physeq, x = opt$x, fill = opt$fill) +
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131 geom_bar(aes(color = NULL, fill = !!sym(opt$fill)), stat = "identity", position = "stack")
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132 } else {
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133 p <- plot_bar(physeq, fill = opt$fill) +
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134 geom_bar(aes(color = NULL, fill = !!sym(opt$fill)), stat = "identity", position = "stack")
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135 }
3
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136
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137 # Only facet if the facet variable is provided and exists in the sample data
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138 if (!is.null(opt$facet) && opt$facet != "") {
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139 if (opt$facet %in% sample_vars) {
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140 p <- p + facet_wrap(as.formula(paste("~", opt$facet)))
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141 } else {
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142 warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped."))
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143 }
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144 }
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145
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146
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147 # Save to output file
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148 ggsave(
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149 filename = opt$output,
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150 plot = p,
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151 width = opt$width,
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152 height = opt$height,
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153 device = opt$device
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154 )