Plot ragtag paf

tools/plot_ragtag_paf/.shed.yml

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+categories:
+  - Assembly
+  - Visualization
+description: Plot RagTag output to compare query contigs against the reference
+exclude:
+  - tool_test_output.html
+  - tool_test_output.json
+homepage_url: http://github.com/usegalaxy-au/tools-au
+long_description: Plot RagTag output to compare query contigs against the reference
+name: plot_ragtag_paf
+owner: galaxy-australia
+remote_repository_url: https://github.com/usegalaxy-au/tools-au

tools/plot_ragtag_paf/plot_ragtag_paf.R

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+#!/usr/bin/env Rscript
+
+options(
+    show.error.messages = FALSE,
+    error = function() {
+        cat(geterrmessage(), file = stderr())
+        q("no", 1, FALSE)
+    }
+)
+
+library(data.table)
+library(ggplot2)
+library(pafr)
+library(viridisLite)
+library(yaml)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+#############
+# FUNCTIONS #
+#############
+
+
+# Adjust the PAF coordinates to the continuous x-axis
+adjust_coords <- function(qname, qstart, qend, tname, tstart, tend) {
+    my_qstart <- lookup_qstart(qname)
+    my_tstart <- lookup_tstart(tname)
+    return(
+        data.table(
+            adj_qstart = qstart + my_qstart,
+            adj_qend = qend + my_qstart,
+            adj_tstart = tstart + my_tstart,
+            adj_tend = tend + my_tstart
+        )
+    )
+}
+
+# calculate spacing between contigs so the ref and query take up the same x-axis
+# space
+get_padding <- function(paf) {
+    tlen_sum <- unique(paf, by = "tname")[, sum(tlen)]
+    tgaps_total <- paf[, length(unique(tname))]
+
+    qlen_sum <- unique(paf, by = "qname")[, sum(qlen)]
+    qgaps_total <- paf[, length(unique(qname))]
+
+    # the minumum gap is going to be one tenth of the x-axis space
+    if (tlen_sum > qlen_sum) {
+        min_gap <- (tlen_sum * gap_size) / tgaps_total
+        full_tlen <- tlen_sum + (tgaps_total * min_gap)
+
+        total_qpadding <- full_tlen - qlen_sum
+        return(
+            c(
+                "t_padding" = min_gap,
+                "q_padding" = total_qpadding / qgaps_total
+            )
+        )
+    } else if (tlen_sum < qlen_sum) {
+        min_gap <- (qlen_sum * gap_size) / qgaps_total
+        full_qlen <- qlen_sum + (qgaps_total * min_gap)
+
+        total_tpadding <- full_qlen - tlen_sum
+
+        return(
+            c(
+                "t_padding" = total_tpadding / tgaps_total,
+                "q_padding" = min_gap
+            )
+        )
+    } else {
+        min_gap <- (tlen_sum * gap_size) / tgaps_total
+        return(
+            c(
+                "t_padding" = min_gap,
+                "q_padding" = min_gap
+            )
+        )
+    }
+}
+
+# offsets for the adjusted coordinates
+lookup_tstart <- function(x) {
+    return(unique(tstarts[tname == x, shift_tstart]))
+}
+
+
+lookup_qstart <- function(x) {
+    return(unique(qstarts[qname == x, shift_qstart]))
+}
+
+
+###########
+# GLOBALS #
+###########
+
+# PAF column spec
+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)
+
+########
+# MAIN #
+########
+
+# read the 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
+padding <- get_padding(paf_dt[tp == "P" & nmatch >= min_nmatch])
+
+# order the reference contigs
+paf_dt[, tname := factor(tname, levels = gtools::mixedsort(unique(tname)))]
+setkeyv(paf_dt, cols = sort_columns)
+
+# generate continuous  reference coordinates
+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)]
+tpaf[, pad_tend := shift_tstart + tlen]
+
+# order the query contigs by their position in the AGP file
+query_order <- agp[, V6]
+
+query_paf <- paf_dt[qname %in% query_order & tp == "P" & nmatch >= min_nmatch]
+subset_query_order <- query_order[query_order %in% query_paf[, qname]]
+
+# Map query contigs onto a universal x-scale
+query_paf[, qname := factor(qname, levels = subset_query_order)]
+setkeyv(query_paf, cols = sort_columns)
+
+qpaf <- unique(query_paf, by = "qname")
+qpaf[, pad_qstart := shift(cumsum(qlen + padding[["q_padding"]]), 1, 0)]
+qpaf[, shift_qstart := pad_qstart + (padding[["q_padding"]] / 2)]
+qpaf[, pad_qend := shift_qstart + qlen]
+
+# generate offsets for the alignment records
+tstarts <- unique(tpaf[, .(tname, shift_tstart)])
+qstarts <- unique(qpaf[, .(qname, shift_qstart)])
+
+# adjust the alignment coordinates
+paf_dt[,
+    c(
+        "adj_qstart",
+        "adj_qend",
+        "adj_tstart",
+        "adj_tend"
+    ) := adjust_coords(qname, qstart, qend, tname, tstart, tend),
+    by = .(qname, qstart, qend, tname, tstart, tend)
+]
+
+# generate polygons. P is for primary alignments only
+polygon_y_bump <- 0.017 # account for contig thickness
+paf_polygons <- paf_dt[
+    tp == "P" & nmatch >= min_nmatch,
+    .(
+        x = c(adj_tstart, adj_qstart, adj_qend, adj_tend),
+        y = c(
+            t_y + polygon_y_bump,
+            q_y - polygon_y_bump,
+            q_y - polygon_y_bump,
+            t_y + polygon_y_bump
+        ),
+        id = paste0("polygon", .GRP)
+    ),
+    by = .(qname, qstart, qend, tname, tstart, tend)
+]
+
+# set up plot
+total_height <- (q_y - t_y) * 1.618
+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
+)
+names(all_colours) <- c(
+    "query",
+    rep("blank", palette_space),
+    all_contig_names
+)
+
+# Plot the ideogram with ribbons connecting the two sets of contigs
+gp <- ggplot() +
+    theme_void(base_family = "Lato", base_size = 12) +
+    scale_fill_manual(
+        values = all_colours, guide = "none"
+    ) +
+    scale_colour_manual(
+        values = all_colours, guide = "none"
+    ) +
+    geom_polygon(
+        data = paf_polygons,
+        aes(
+            x = x, y = y, group = id, fill = tname
+        ), alpha = 0.5
+    ) +
+    geom_segment(
+        data = tpaf,
+        aes(
+            x = shift_tstart,
+            xend = pad_tend,
+            colour = tname
+        ),
+        y = t_y,
+        linewidth = 5,
+        lineend = "butt"
+    ) +
+    geom_segment(
+        data = qpaf,
+        aes(
+            x = shift_qstart,
+            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),
+        hjust = 0.5,
+        vjust = 0.5
+    ) +
+    annotate(
+        geom = "text",
+        label = "Reference contigs",
+        x = middle_x,
+        y = t_y - (y_axis_space / 3),
+        hjust = 0.5,
+        vjust = 0.5
+    )
+
+ggsave(plot_file,
+    gp,
+    width = plot_width,
+    height = plot_height,
+    units = "mm",
+    device = cairo_pdf
+)
+
+sessionInfo()

tools/plot_ragtag_paf/plot_ragtag_paf.xml

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+<tool id="plot_ragtag_paf" name="Plot RagTag output" version="0.0.1">
+    <description>to compare query contigs to the reference</description>
+    <requirements>
+        <requirement type="package" version="0.0.2">r-pafr</requirement>
+        <requirement type="package" version="0.4.2">r-viridislite</requirement>
+        <requirement type="package" version="1.15.4">r-data.table</requirement>
+        <requirement type="package" version="2.3.10">r-yaml</requirement>
+        <requirement type="package" version="3.5.1">r-ggplot2</requirement>
+        <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>
+    <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}'
+        </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"/>
+        <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="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>
+        <data name="plot" format="pdf" label="${tool.name} on ${on_string}" from_work_dir="ragtag.pdf"/>
+    </outputs>
+    <tests>
+        <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"/>
+            <output name="plot">
+                <assert_contents>
+                    <has_size size="8758" delta="1000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        Accepts the PAF and AGP produced by the RagTag Scaffold and draws a plot
+        showing the alignment of the query contigs to the reference contigs.
+
+        .. figure:: $PATH_TO_IMAGES/ragtag.png
+           :alt: RagTag plot
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{plot_ragtag_paf,
+                title = {plot_ragtag_paf},
+                author = {Harrop, Tom},
+                year = {2024},
+                organization = {Galaxy Australia},
+                url = {https://github.com/usegalaxy-au/tools-au},
+                }
+        </citation>
+    </citations>
+</tool>