Merge pull request #6665 from MaraBesemer/main

add: variables topX and normalize to Phyloseq Bar Plot
galaxyproject · Jan 10, 2025 · 26f87cc · 26f87cc
2 parents 637a6eb + 8282568
commit 26f87cc
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Showing 2 changed files with 140 additions and 40 deletions.
diff --git a/tools/phyloseq/phyloseq_plot_bar.R b/tools/phyloseq/phyloseq_plot_bar.R
@@ -26,6 +26,34 @@ option_list <- list(
     make_option(c("--output"),
         action = "store", dest = "output",
         help = "Output file (PDF)"
+    ),
+    make_option(c("--topX"),
+        action = "store", dest = "topX", default = NULL,
+        help = "Show only the top X taxa based on abundance (e.g., '10') (optional)"
+    ),
+    make_option(c("--keepOthers"),
+        action = "store_true", dest = "keepOthers", default = FALSE,
+        help = "Keep taxa not in topX and label them as 'Others' (optional)"
+    ),
+    make_option(c("--keepNonAssigned"),
+        action = "store_true", dest = "keepNonAssigned", default = FALSE,
+        help = "Keep taxa labeled as 'Not Assigned' (optional)"
+    ),
+    make_option(c("--normalize"),
+        action = "store_true", dest = "normalize", default = FALSE,
+        help = "Normalize abundances to sum to 100% (optional)"
+    ),
+    make_option(c("--width"),
+        action = "store", dest = "width", default = 10,
+        type = "numeric", help = "Width of the output plot in inches"
+    ),
+    make_option(c("--height"),
+        action = "store", dest = "height", default = 8,
+        type = "numeric", help = "Height of the output plot in inches"
+    ),
+    make_option(c("--device"),
+        action = "store", dest = "device", default = "pdf",
+        help = "Output format (e.g., 'pdf', 'png', 'jpeg')"
     )
 )
 
@@ -38,9 +66,6 @@ opt <- args$options
 if (is.null(opt$input) || opt$input == "") {
     stop("Error: Input file is required.")
 }
-if (is.null(opt$x) || opt$x == "") {
-    stop("Error: X-axis variable is required.")
-}
 if (is.null(opt$output) || opt$output == "") {
     stop("Error: Output file is required.")
 }
@@ -49,14 +74,63 @@ if (is.null(opt$output) || opt$output == "") {
 print(paste("Trying to read:", opt$input))
 physeq <- readRDS(opt$input)
 
+# Normalize to relative abundances if requested
+if (opt$normalize) {
+    print("Normalizing abundances to sum to 100%...")
+    physeq <- transform_sample_counts(physeq, function(x) 100 * x / sum(x))
+}
+
+if (opt$keepNonAssigned) {
+    # Add synthetic "Not Assigned" for missing/NA taxa
+    tax_table(physeq) <- apply(tax_table(physeq), c(1, 2), function(x) ifelse(is.na(x) | x == "", "Not Assigned", x))
+}
 # Check if the 'x' and 'fill' variables are valid
 sample_vars <- colnames(sample_data(physeq))
-if (!opt$x %in% sample_vars) {
-    stop(paste("Error: X-axis variable", opt$x, "does not exist in the sample data."))
+
+# If topX is provided, filter the phyloseq object to show only top X taxa
+if (!is.null(opt$topX) && opt$topX != "") {
+    topX <- as.numeric(opt$topX)
+    if (is.na(topX) || topX <= 0) {
+        stop("Error: topX should be a positive number.")
+    }
+
+    # Aggregate the data at the selected rank (e.g., Phylum)
+    tax_rank <- opt$fill # Adjust as necessary
+    physeq_agg <- tax_glom(physeq, taxrank = tax_rank)
+
+    # Get the abundance of each taxon at the selected rank
+    taxa_abundance <- taxa_sums(physeq_agg)
+
+    # Summarize the abundance at each taxonomic rank (grouping by taxonomic name)
+    tax_table_agg <- tax_table(physeq_agg)
+    taxa_abundance_by_rank <- tapply(taxa_abundance, tax_table_agg[, tax_rank], sum)
+
+    # Identify the top X taxa by summed abundance
+    top_taxa <- names(sort(taxa_abundance_by_rank, decreasing = TRUE))[1:topX]
+
+    print("Only plotting taxa in TopX taxa group:")
+    print(top_taxa)
+
+    # Get the OTUs corresponding to the top taxa
+    otus_in_top_taxa <- rownames(tax_table_agg)[tax_table_agg[, tax_rank] %in% top_taxa]
+
+    if (opt$keepOthers) {
+        # Label taxa not in top_taxa as "Others"
+        tax_table(physeq_agg)[, tax_rank][!rownames(tax_table(physeq_agg)) %in% otus_in_top_taxa] <- "Others"
+        physeq <- physeq_agg
+    } else {
+        # Subset the phyloseq object to keep only the top X taxa
+        physeq_filtered <- prune_taxa(otus_in_top_taxa, physeq_agg)
+        physeq <- physeq_filtered
+    }
 }
 
 # Generate bar plot
-p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
+if (!is.null(opt$x) && opt$x != "") {
+    p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
+} else {
+    p <- plot_bar(physeq, fill = opt$fill) # If no x is provided, don't include x
+}
 
 # Only facet if the facet variable is provided and exists in the sample data
 if (!is.null(opt$facet) && opt$facet != "") {
@@ -67,8 +141,11 @@ if (!is.null(opt$facet) && opt$facet != "") {
     }
 }
 
-# Save to output file using PDF device
-print(paste("Saving plot to:", opt$output))
-pdf(file = opt$output, width = 10, height = 8)
-print(p)
-dev.off()
+# Save to output file
+ggsave(
+    filename = opt$output,
+    plot = p,
+    width = opt$width,
+    height = opt$height,
+    device = opt$device
+)
diff --git a/tools/phyloseq/phyloseq_plot_bar.xml b/tools/phyloseq/phyloseq_plot_bar.xml
@@ -12,44 +12,66 @@ Rscript '${__tool_directory__}/phyloseq_plot_bar.R'
 --fill '$fill'
 --facet '${facet}'
 --output '$output'
+--topX '${topX}'
+--keepOthers '${keepOthers}'
+--keepNonAssigned '${keepNonAssigned}'
+--normalize '${normalize}'
+--width '${width}'
+--height '${height}'
+--device '${device}'
   ]]></command>
   <inputs>
     <expand macro="phyloseq_input"/>
-    <param name="x" type="text" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum)" />
-    <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)" />
-    <param name="facet" type="text" optional="true" label="Facet by variable" help="Optional: Variable to facet the chart by (e.g., SampleType)" />
+    <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum). If not specified, the Samples are taken." />
+    <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)." />
+    <param name="facet" type="text" optional="true" label="Facet by variable" help="Variable to facet the chart by (e.g., SampleType)." />
+    <param name="topX" value="10" type="integer" optional="true" label="Top X" help="Only show the ranks with the top X abundance." />
+    <param name="keepOthers" type="boolean" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
+    <param name="keepNonAssigned" type="boolean" label="Keep Non Assigned" help="Keep OTUs that are not assigned at this rank and label as 'Not Assigned'." />
+    <param name="normalize" type="boolean" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." />
+    <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." />
+    <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." />
+    <param name="device" type="select" value="pdf" label="Output Device" help="Device to use for the output file. Options include pdf, png, and others.">
+      <option value="pdf">PDF</option>
+      <option value="png">PNG</option>
+      <option value="jpeg">JPEG</option>
+      <option value="tiff">TIFF</option>
+    </param>
   </inputs>
   <outputs>
     <data name="output" format="pdf" label="Bar Chart (PDF)" />
   </outputs>
-   <tests>
-    <!-- Test 1: Default parameters -->
+  <tests>
+    <!-- Test 1: Basic functionality with x and fill variables -->
     <test>
-        <param name="input" value="output.phyloseq" ftype="phyloseq"/>
-        <param name="x" value="Property"/>
-        <param name="fill" value="Number"/>
-        <param name="facet" value="Property"/>
-        <output name="output" ftype="pdf">
-            <assert_contents>
-                <has_text text="%PDF"/>
-                <has_text text="%%EOF"/>
-            </assert_contents>
-        </output>
+      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+      <param name="x" value="Property"/>
+      <param name="fill" value="Phylum"/>
+      <param name="device" value="pdf"/>
+      <output name="output" ftype="pdf">
+        <assert_contents>
+          <has_text text="%PDF"/>
+          <has_text text="%%EOF"/>
+        </assert_contents>
+      </output>
     </test>
-    <!-- Test 2: Valid parameters without facet -->
+
+    <!-- Test 2: TopX filtering and normalization -->
     <test>
-        <param name="input" value="output.phyloseq" ftype="phyloseq"/>
-        <param name="x" value="Property"/>
-        <param name="fill" value="Number"/>
-        <param name="facet" value=""/>
-        <output name="output" ftype="pdf">
-            <assert_contents>
-                <has_text text="%PDF"/>
-                <has_text text="%%EOF"/>
-            </assert_contents>
-        </output>
+      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+      <param name="x" value="Property"/>
+      <param name="fill" value="Genus"/>
+      <param name="facet" value="SampleType"/>
+      <param name="topX" value="10"/>
+      <param name="normalize" value="true"/>
+      <output name="output" ftype="pdf">
+        <assert_contents>
+          <has_text text="%PDF"/>
+          <has_text text="%%EOF"/>
+        </assert_contents>
+      </output>
     </test>
-</tests>
+  </tests>
 
   <help>
     **Description**
@@ -62,15 +84,16 @@ Rscript '${__tool_directory__}/phyloseq_plot_bar.R'
     - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum).
     - **Fill variable**: (Optional) The variable to use for the bar fill colors (e.g., Genus, Order).
     - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
+    - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
+    - **Device**: Output format (e.g., pdf, png, jpeg, tiff).
 
     **Outputs**
 
-    - A PDF file containing the bar chart.
+    - A file containing the bar chart in the specified format.
 
     **Usage Notes**
 
     Ensure that the input file is a valid phyloseq object in RDS format.
   </help>
   <expand macro="citations"/>
 </tool>
-