Mercurial > repos > galaxy-australia > plot_ragtag_paf

changeset 1:94e0834ae4ed draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c0fbce102933ff20902a65795000339a8314d12e
author galaxy-australia
date Mon, 14 Oct 2024 02:33:22 +0000
parents 664d63b0e817
children c1bed78b9ed5
files plot_ragtag_paf.R plot_ragtag_paf.xml
diffstat 2 files changed, 145 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/plot_ragtag_paf.R	Wed Sep 25 07:52:38 2024 +0000
+++ b/plot_ragtag_paf.R	Mon Oct 14 02:33:22 2024 +0000
@@ -98,20 +98,35 @@
 sort_columns <- c("tname", "tstart", "tend", "qname", "qstart", "qend")
 
 config_file <- args[1]
-config <- yaml.load_file(config_file)
-typed_config <- lapply(config, type.convert, as.is = TRUE)
-list2env(typed_config, envir = .GlobalEnv)
+
+# fixed plotting paramaters
+t_y <- 1
+q_y <- 2
 
 ########
 # MAIN #
 ########
 
+# process the config
+message("Reading the plot config")
+config <- yaml.load_file(config_file)
+typed_config <- lapply(config, type.convert, as.is = TRUE)
+invisible(
+    list2env(
+        typed_config,
+        envir = .GlobalEnv
+    )
+)
+
+
 # read the data
+message("Reading the plot data")
 agp <- fread(agp_file, fill = TRUE, skip = 2)[!V5 %in% c("N", "U")]
 raw_paf <- read_paf(paf_file)
 paf_dt <- data.table(raw_paf)
 
 # calculate spacing
+message("Calculating spacing between contigs")
 padding <- get_padding(paf_dt[tp == "P" & nmatch >= min_nmatch])
 
 # order the reference contigs
@@ -119,6 +134,7 @@
 setkeyv(paf_dt, cols = sort_columns)
 
 # generate continuous  reference coordinates
+message("Generating coordinates for contigs")
 tpaf <- unique(paf_dt, by = "tname")
 tpaf[, pad_tstart := shift(cumsum(tlen + padding[["t_padding"]]), 1, 0)]
 tpaf[, shift_tstart := pad_tstart + (padding[["t_padding"]] / 2)]
@@ -140,6 +156,7 @@
 qpaf[, pad_qend := shift_qstart + qlen]
 
 # generate offsets for the alignment records
+message("Generating coordinates for alignments")
 tstarts <- unique(tpaf[, .(tname, shift_tstart)])
 qstarts <- unique(qpaf[, .(qname, shift_qstart)])
 
@@ -155,6 +172,7 @@
 ]
 
 # generate polygons. P is for primary alignments only
+message("Generating polygons for alignments")
 polygon_y_bump <- 0.017 # account for contig thickness
 paf_polygons <- paf_dt[
     tp == "P" & nmatch >= min_nmatch,
@@ -176,8 +194,6 @@
 y_axis_space <- (total_height - (q_y - t_y)) / 2
 middle_x <- tpaf[1, shift_tstart] + tpaf[.N, pad_tend] / 2
 
-
-
 all_contig_names <- c(tpaf[, unique(tname)])
 all_colours <- viridis(
     length(all_contig_names) + palette_space + 1
@@ -188,9 +204,12 @@
     all_contig_names
 )
 
-# Plot the ideogram with ribbons connecting the two sets of contigs
+# Plot the ideogram with ribbons connecting the two sets of contigs. To
+# accomodate upside plots we have to draw the polygons first then add the
+# contigs later
+message("Plotting")
 gp <- ggplot() +
-    theme_void(base_family = "Lato", base_size = 12) +
+    theme_void(base_family = "Lato", base_size = fontsize) +
     scale_fill_manual(
         values = all_colours, guide = "none"
     ) +
@@ -207,10 +226,10 @@
         data = tpaf,
         aes(
             x = shift_tstart,
+            y = t_y,
             xend = pad_tend,
             colour = tname
         ),
-        y = t_y,
         linewidth = 5,
         lineend = "butt"
     ) +
@@ -218,22 +237,21 @@
         data = qpaf,
         aes(
             x = shift_qstart,
+            y = q_y,
             xend = pad_qend
         ),
         colour = all_colours[["query"]],
-        y = q_y,
         linewidth = 5,
         lineend = "butt"
     ) +
-    ylim(
-        t_y - y_axis_space,
-        q_y + y_axis_space
-    ) +
     annotate(
         geom = "text",
         label = "Query contigs",
         x = middle_x,
-        y = q_y + (y_axis_space / 3),
+        y = ifelse(label_query_contigs == TRUE,
+            q_y + (y_axis_space * 2 / 3),
+            q_y + (y_axis_space / 3)
+        ),
         hjust = 0.5,
         vjust = 0.5
     ) +
@@ -241,11 +259,61 @@
         geom = "text",
         label = "Reference contigs",
         x = middle_x,
-        y = t_y - (y_axis_space / 3),
+        y = ifelse(label_ref_contigs == TRUE,
+            t_y - (y_axis_space * 2 / 3),
+            t_y - (y_axis_space / 3)
+        ),
         hjust = 0.5,
         vjust = 0.5
     )
 
+# Reverse the scales and the limits to plot reference on top
+if (upside_down == TRUE) {
+    gp <- gp + scale_y_continuous(
+        limits = c(
+            q_y + y_axis_space,
+            t_y - y_axis_space
+        ),
+        transform = "reverse"
+    )
+} else {
+    gp <- gp + scale_y_continuous(
+        limits = c(
+            t_y - y_axis_space,
+            q_y + y_axis_space
+        )
+    )
+}
+
+# reference contig names
+if (label_ref_contigs == TRUE) {
+    gp <- gp + geom_text(
+        data = tpaf,
+        aes(
+            x = (shift_tstart + pad_tend) / 2,
+            y = t_y - (2.5 * polygon_y_bump),
+            label = tname
+        ),
+        angle = 30,
+        hjust = ifelse(upside_down == TRUE, 0, 1)
+    )
+}
+
+# query contig names
+if (label_query_contigs == TRUE) {
+    gp <- gp + geom_text(
+        data = qpaf,
+        aes(
+            x = (shift_qstart + pad_qend) / 2,
+            y = q_y + (2.5 * polygon_y_bump),
+            label = qname
+        ),
+        angle = 30,
+        hjust = ifelse(upside_down == TRUE, 1, 0),
+    )
+}
+
+message("Writing the plot to file")
 ggsave(plot_file,
     gp,
     width = plot_width,
@@ -254,4 +322,8 @@
     device = cairo_pdf
 )
 
+# Print session info to stderr
+message("\nsessionInfo():\n")
+sink(stderr())
 sessionInfo()
+sink()
--- a/plot_ragtag_paf.xml	Wed Sep 25 07:52:38 2024 +0000
+++ b/plot_ragtag_paf.xml	Mon Oct 14 02:33:22 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="plot_ragtag_paf" name="Plot RagTag output" version="0.0.1">
+<tool id="plot_ragtag_paf" name="Plot RagTag output" version="0.0.2" profile="24.1" license="MIT">
     <description>to compare query contigs to the reference</description>
     <requirements>
         <container type="docker">ghcr.io/tomharrop/r-containers:r2u_24.04_cv1</container>
@@ -12,37 +12,54 @@
         <!-- <requirement type="package" version="3.9.5">r-gtools</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-Rscript 
-'${__tool_directory__}/plot_ragtag_paf.R'
-'${plot_config}'
-            ]]></command>
+
+    ## Suppress R warnings about container
+    if [ -f /etc/R/Rprofile.site ]; then
+        sed -i 
+        '/options(bspm.version.check=FALSE)/i options(bspm.sudo = TRUE)' 
+        /etc/R/Rprofile.site ;
+    fi ;
+
+    ## Print the plot config to stderr
+    sed -e 's/^[ \t]*//' -e '/^$/d' '${plot_config}' > config.yaml &&
+    echo "PLOT CONFIG:" >&2 &&
+    cat config.yaml >&2 &&
+
+    ## Draw the plot
+    printf '\n%s\n' "Running plot_ragtag_paf.R"  >&2 &&
+    Rscript 
+    '${__tool_directory__}/plot_ragtag_paf.R'
+    config.yaml
+    ]]></command>
     <configfiles>
         <configfile name="plot_config">
-agp_file: '${input_agp}'
-paf_file: '${input_paf}'
-plot_file: 'ragtag.pdf'
-fontsize: '${plot_params.fontsize}'
-gap_size: '${plot_params.gap_size}'
-min_nmatch: '${min_nmatch}'
-palette_space: '${plot_params.palette_space}'
-plot_height: '${plot_params.plot_height}'
-plot_width: '${plot_params.plot_width}'
-q_y: '${plot_params.q_y}'
-t_y: '${plot_params.t_y}'
+            agp_file: '${input_agp}'
+            paf_file: '${input_paf}'
+            plot_file: 'ragtag.pdf'
+            fontsize: '${plot_params.fontsize}'
+            gap_size: '${plot_params.gap_size}'
+            min_nmatch: '${min_nmatch}'
+            palette_space: '${plot_params.palette_space}'
+            plot_height: '${plot_params.plot_height}'
+            plot_width: '${plot_params.plot_width}'
+            label_ref_contigs: '${plot_params.label_ref_contigs}'
+            label_query_contigs: '${plot_params.label_query_contigs}'
+            upside_down: '${upside_down}'
         </configfile>
     </configfiles>
     <inputs>
         <param format="paf" name="input_paf" label="PAF output from RagTag" type="data"/>
         <param format="agp" name="input_agp" label="AGP output from RagTag" type="data"/>
         <param type="integer" name="min_nmatch" label="Minimum alignment length to include in plot" value="20000"/>
+        <param type="boolean" name="upside_down" label="Plot the reference contigs on top" value="false" truevalue="TRUE" falsevalue="FALSE"/>
         <section name="plot_params" title="Plot parameters">
             <param type="integer" name="plot_width" label="Plot width (mm)" value="254"/>
             <param type="integer" name="plot_height" label="Plot height (mm)" value="191"/>
             <param type="integer" name="fontsize" label="Fontsize (pt)" value="12"/>
+            <param type="boolean" name="label_ref_contigs" label="Print the names of the reference contigs" value="false" truevalue="TRUE" falsevalue="FALSE"/>
+            <param type="boolean" name="label_query_contigs" label="Print the names of the query contigs" value="false" truevalue="TRUE" falsevalue="FALSE"/>
             <param type="integer" name="palette_space" label="Number of unused colours in the colour palette between the query contig colour and the colour of the first reference contig." help="Try a higher value if the query contigs look too similar to the reference contigs." value="4"/>
             <param type="float" min="0" max="1" name="gap_size" label="Total length of gaps between contigs relative to the total assembly length." help="Try a higher value if the contigs look too close together." value="0.1"/>
-            <param type="integer" name="t_y" label="Position of reference contigs on the y-axis" value="1"/>
-            <param type="integer" name="q_y" label="Position of query contigs on the y-axis" value="2"/>
         </section>
     </inputs>
     <outputs>
@@ -54,7 +71,29 @@
             <param name="input_agp" ftype="agp" value="ragtag.agp"/>
             <output name="plot">
                 <assert_contents>
-                    <has_size size="8758" delta="1000" />
+                    <has_size size="8758" delta="1000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_paf" ftype="paf.gz" value="ragtag.paf.gz"/>
+            <param name="input_agp" ftype="agp" value="ragtag.agp"/>
+            <param name="upside_down" value="true"/>
+            <output name="plot">
+                <assert_contents>
+                    <has_size size="8756" delta="1000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_paf" ftype="paf.gz" value="ragtag.paf.gz"/>
+            <param name="input_agp" ftype="agp" value="ragtag.agp"/>
+            <param name="upside_down" value="true"/>
+            <param name="label_query_contigs" value="true"/>
+            <param name="label_ref_contigs" value="true"/>
+            <output name="plot">
+                <assert_contents>
+                    <has_size size="11159" delta="1000"/>
                 </assert_contents>
             </output>
         </test>