Mercurial > repos > iuc > phyloseq_plot_ordination

comparison phyloseq_plot_bar.R @ 7:eab0b21652c4 draft default tip

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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 17:12:09 +0000
parents f9543efabd85
children
comparison
equal deleted inserted replaced
6:f9543efabd85 7:eab0b21652c4
125 } 125 }
126 } 126 }
127 127
128 # Generate bar plot 128 # Generate bar plot
129 if (!is.null(opt$x) && opt$x != "") { 129 if (!is.null(opt$x) && opt$x != "") {
130 p <- plot_bar(physeq, x = opt$x, fill = opt$fill) 130 p <- plot_bar(physeq, x = opt$x, fill = opt$fill) +
131 geom_bar(aes(color = NULL, fill = !!sym(opt$fill)), stat = "identity", position = "stack")
131 } else { 132 } else {
132 p <- plot_bar(physeq, fill = opt$fill) # If no x is provided, don't include x 133 p <- plot_bar(physeq, fill = opt$fill) +
134 geom_bar(aes(color = NULL, fill = !!sym(opt$fill)), stat = "identity", position = "stack")
133 } 135 }
134 136
135 # Only facet if the facet variable is provided and exists in the sample data 137 # Only facet if the facet variable is provided and exists in the sample data
136 if (!is.null(opt$facet) && opt$facet != "") { 138 if (!is.null(opt$facet) && opt$facet != "") {
137 if (opt$facet %in% sample_vars) { 139 if (opt$facet %in% sample_vars) {
139 } else { 141 } else {
140 warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped.")) 142 warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped."))
141 } 143 }
142 } 144 }
143 145
146
144 # Save to output file 147 # Save to output file
145 ggsave( 148 ggsave(
146 filename = opt$output, 149 filename = opt$output,
147 plot = p, 150 plot = p,
148 width = opt$width, 151 width = opt$width,