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changeset 0:664d63b0e817 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 1d55571817c874123ca77eb12c8e579aa936eeab
author galaxy-australia
date Wed, 25 Sep 2024 07:52:38 +0000
parents
children 94e0834ae4ed
files plot_ragtag_paf.R plot_ragtag_paf.xml static/images/ragtag.png test-data/ragtag.agp test-data/ragtag.paf.gz
diffstat 5 files changed, 496 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_ragtag_paf.R	Wed Sep 25 07:52:38 2024 +0000
@@ -0,0 +1,257 @@
+#!/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()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_ragtag_paf.xml	Wed Sep 25 07:52:38 2024 +0000
@@ -0,0 +1,81 @@
+<tool id="plot_ragtag_paf" name="Plot RagTag output" version="0.0.1">
+    <description>to compare query contigs to the reference</description>
+    <requirements>
+        <container type="docker">ghcr.io/tomharrop/r-containers:r2u_24.04_cv1</container>
+        <!-- The following requirements work but the fonts aren't configured
+        correctly -->
+        <!-- <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>
Binary file static/images/ragtag.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ragtag.agp	Wed Sep 25 07:52:38 2024 +0000
@@ -0,0 +1,158 @@
+## agp-version 2.1
+# AGP created by RagTag v2.1.0
+1_RagTag	1	243556	1	W	contig_63	1	243556	-
+1_RagTag	243557	243656	2	U	100	scaffold	yes	align_genus
+1_RagTag	243657	769839	3	W	contig_62	1	526183	+
+1_RagTag	769840	769939	4	U	100	scaffold	yes	align_genus
+1_RagTag	769940	1077133	5	W	contig_100	1	307194	-
+1_RagTag	1077134	1077233	6	U	100	scaffold	yes	align_genus
+1_RagTag	1077234	1080142	7	W	contig_80	1	2909	-
+1_RagTag	1080143	1080242	8	U	100	scaffold	yes	align_genus
+1_RagTag	1080243	1753612	9	W	contig_60	1	673370	+
+1_RagTag	1753613	1754048	10	N	436	scaffold	yes	align_genus
+1_RagTag	1754049	2012384	11	W	contig_16	1	258336	+
+1_RagTag	2012385	2086929	12	N	74545	scaffold	yes	align_genus
+1_RagTag	2086930	4693729	13	W	contig_38	1	2606800	-
+2_RagTag	1	12683	1	W	contig_96	1	12683	-
+2_RagTag	12684	12783	2	U	100	scaffold	yes	align_genus
+2_RagTag	12784	1826104	3	W	contig_30	1	1813321	+
+2_RagTag	1826105	1862437	4	N	36333	scaffold	yes	align_genus
+2_RagTag	1862438	1863805	5	W	contig_11	1	1368	-
+2_RagTag	1863806	1877480	6	N	13675	scaffold	yes	align_genus
+2_RagTag	1877481	2472318	7	W	contig_8	1	594838	-
+2_RagTag	2472319	2472418	8	U	100	scaffold	yes	align_genus
+2_RagTag	2472419	2480086	9	W	contig_103	1	7668	-
+2_RagTag	2480087	2480186	10	U	100	scaffold	yes	align_genus
+2_RagTag	2480187	3401419	11	W	contig_102	1	921233	-
+2_RagTag	3401420	3401519	12	U	100	scaffold	yes	align_genus
+2_RagTag	3401520	3987789	13	W	contig_64	1	586270	+
+2_RagTag	3987790	3987889	14	U	100	scaffold	yes	align_genus
+2_RagTag	3987890	4003446	15	W	contig_95	1	15557	+
+2_RagTag	4003447	4003546	16	U	100	scaffold	yes	align_genus
+2_RagTag	4003547	4302373	17	W	contig_46	1	298827	-
+2_RagTag	4302374	4302473	18	U	100	scaffold	yes	align_genus
+2_RagTag	4302474	4416170	19	W	contig_75	1	113697	+
+2_RagTag	4416171	4435718	20	N	19548	scaffold	yes	align_genus
+2_RagTag	4435719	4707751	21	W	contig_93	1	272033	+
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+2_RagTag	4707852	4709556	23	W	contig_131	1	1705	-
+2_RagTag	4709557	4709656	24	U	100	scaffold	yes	align_genus
+2_RagTag	4709657	4877510	25	W	contig_83	1	167854	-
+3_RagTag	1	1230166	1	W	contig_67	1	1230166	-
+3_RagTag	1230167	1251655	2	N	21489	scaffold	yes	align_genus
+3_RagTag	1251656	1257278	3	W	contig_135	1	5623	+
+3_RagTag	1257279	1257378	4	U	100	scaffold	yes	align_genus
+3_RagTag	1257379	1260195	5	W	contig_105	1	2817	+
+3_RagTag	1260196	1260295	6	U	100	scaffold	yes	align_genus
+3_RagTag	1260296	4010002	7	W	contig_73	1	2749707	-
+3_RagTag	4010003	4017979	8	N	7977	scaffold	yes	align_genus
+3_RagTag	4017980	4032481	9	W	contig_78	1	14502	+
+4_RagTag	1	421154	1	W	contig_53	1	421154	+
+4_RagTag	421155	421254	2	U	100	scaffold	yes	align_genus
+4_RagTag	421255	428922	3	W	contig_128	1	7668	+
+4_RagTag	428923	429022	4	U	100	scaffold	yes	align_genus
+4_RagTag	429023	1107160	5	W	contig_48	1	678138	+
+4_RagTag	1107161	1171788	6	N	64628	scaffold	yes	align_genus
+4_RagTag	1171789	1397297	7	W	contig_54	1	225509	+
+4_RagTag	1397298	1397728	8	N	431	scaffold	yes	align_genus
+4_RagTag	1397729	1457766	9	W	contig_79	1	60038	+
+4_RagTag	1457767	1457866	10	U	100	scaffold	yes	align_genus
+4_RagTag	1457867	1563580	11	W	contig_129	1	105714	-
+4_RagTag	1563581	1563737	12	N	157	scaffold	yes	align_genus
+4_RagTag	1563738	3581177	13	W	contig_57	1	2017440	+
+5_RagTag	1	30814	1	W	contig_120	1	30814	+
+5_RagTag	30815	75326	2	N	44512	scaffold	yes	align_genus
+5_RagTag	75327	160509	3	W	contig_108	1	85183	+
+5_RagTag	160510	160609	4	U	100	scaffold	yes	align_genus
+5_RagTag	160610	1269222	5	W	contig_42	1	1108613	+
+5_RagTag	1269223	1274879	6	N	5657	scaffold	yes	align_genus
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+5_RagTag	2139565	2139664	8	U	100	scaffold	yes	align_genus
+5_RagTag	2139665	2455401	9	W	contig_94	1	315737	+
+5_RagTag	2455402	2455501	10	U	100	scaffold	yes	align_genus
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+6_RagTag	2295398	2295497	12	U	100	scaffold	yes	align_genus
+6_RagTag	2295498	2348024	13	W	contig_87	1	52527	+
+6_RagTag	2348025	2348124	14	U	100	scaffold	yes	align_genus
+6_RagTag	2348125	2924414	15	W	contig_77	1	576290	+
+6_RagTag	2924415	2924514	16	U	100	scaffold	yes	align_genus
+6_RagTag	2924515	2946454	17	W	contig_123	1	21940	-
+6_RagTag	2946455	2946554	18	U	100	scaffold	yes	align_genus
+6_RagTag	2946555	3673848	19	W	contig_55	1	727294	-
+6_RagTag	3673849	3673948	20	U	100	scaffold	yes	align_genus
+6_RagTag	3673949	3844665	21	W	contig_99	1	170717	+
+7_RagTag	1	788918	1	W	contig_44	1	788918	+
+7_RagTag	788919	828815	2	N	39897	scaffold	yes	align_genus
+7_RagTag	828816	1758265	3	W	contig_56	1	929450	+
+8_RagTag	1	495564	1	W	contig_41	1	495564	+
+8_RagTag	495565	495664	2	U	100	scaffold	yes	align_genus
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+8_RagTag	500445	500544	4	U	100	scaffold	yes	align_genus
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+8_RagTag	742186	742405	6	N	220	scaffold	yes	align_genus
+8_RagTag	742406	773752	7	W	contig_76	1	31347	-
+8_RagTag	773753	773852	8	U	100	scaffold	yes	align_genus
+8_RagTag	773853	976942	9	W	contig_66	1	203090	+
+8_RagTag	976943	977042	10	U	100	scaffold	yes	align_genus
+8_RagTag	977043	1832718	11	W	contig_61	1	855676	+
+contig_101_RagTag	1	1302	1	W	contig_101	1	1302	+
+contig_104_RagTag	1	691	1	W	contig_104	1	691	+
+contig_106_RagTag	1	2823	1	W	contig_106	1	2823	+
+contig_109_RagTag	1	2768	1	W	contig_109	1	2768	+
+contig_110_RagTag	1	919	1	W	contig_110	1	919	+
+contig_112_RagTag	1	1174	1	W	contig_112	1	1174	+
+contig_113_RagTag	1	5303	1	W	contig_113	1	5303	+
+contig_114_RagTag	1	2947	1	W	contig_114	1	2947	+
+contig_115_RagTag	1	3079	1	W	contig_115	1	3079	+
+contig_117_RagTag	1	8274	1	W	contig_117	1	8274	+
+contig_119_RagTag	1	6118	1	W	contig_119	1	6118	+
+contig_122_RagTag	1	3904	1	W	contig_122	1	3904	+
+contig_124_RagTag	1	26365	1	W	contig_124	1	26365	+
+contig_126_RagTag	1	1109	1	W	contig_126	1	1109	+
+contig_127_RagTag	1	699	1	W	contig_127	1	699	+
+contig_130_RagTag	1	5634	1	W	contig_130	1	5634	+
+contig_132_RagTag	1	4033	1	W	contig_132	1	4033	+
+contig_134_RagTag	1	2622	1	W	contig_134	1	2622	+
+contig_137_RagTag	1	10758	1	W	contig_137	1	10758	+
+contig_140_RagTag	1	22358	1	W	contig_140	1	22358	+
+contig_142_RagTag	1	6894	1	W	contig_142	1	6894	+
+contig_144_RagTag	1	30504	1	W	contig_144	1	30504	+
+contig_145_RagTag	1	6073	1	W	contig_145	1	6073	+
+contig_17_RagTag	1	3562	1	W	contig_17	1	3562	+
+contig_18_RagTag	1	579	1	W	contig_18	1	579	+
+contig_2_RagTag	1	1966	1	W	contig_2	1	1966	+
+contig_24_RagTag	1	657	1	W	contig_24	1	657	+
+contig_26_RagTag	1	875	1	W	contig_26	1	875	+
+contig_27_RagTag	1	2290	1	W	contig_27	1	2290	+
+contig_28_RagTag	1	973	1	W	contig_28	1	973	+
+contig_3_RagTag	1	1885	1	W	contig_3	1	1885	+
+contig_33_RagTag	1	680	1	W	contig_33	1	680	+
+contig_36_RagTag	1	572	1	W	contig_36	1	572	+
+contig_37_RagTag	1	831	1	W	contig_37	1	831	+
+contig_40_RagTag	1	559	1	W	contig_40	1	559	+
+contig_45_RagTag	1	682	1	W	contig_45	1	682	+
+contig_50_RagTag	1	1846	1	W	contig_50	1	1846	+
+contig_51_RagTag	1	548	1	W	contig_51	1	548	+
+contig_6_RagTag	1	822	1	W	contig_6	1	822	+
+contig_68_RagTag	1	1319	1	W	contig_68	1	1319	+
+contig_69_RagTag	1	28525	1	W	contig_69	1	28525	+
+contig_7_RagTag	1	1050	1	W	contig_7	1	1050	+
+contig_71_RagTag	1	8337	1	W	contig_71	1	8337	+
+contig_72_RagTag	1	1700	1	W	contig_72	1	1700	+
+contig_74_RagTag	1	7707	1	W	contig_74	1	7707	+
+contig_81_RagTag	1	9978	1	W	contig_81	1	9978	+
+contig_9_RagTag	1	2661	1	W	contig_9	1	2661	+
+contig_97_RagTag	1	2205	1	W	contig_97	1	2205	+
Binary file test-data/ragtag.paf.gz has changed