contig labels

usegalaxy-au · Oct 14, 2024 · 3e95b33 · 3e95b33
1 parent a1eb60b
commit 3e95b33
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Showing 3 changed files with 53 additions and 16 deletions.
diff --git a/tools/plot_ragtag_paf/plot_ragtag_paf.R b/tools/plot_ragtag_paf/plot_ragtag_paf.R
@@ -209,7 +209,7 @@ names(all_colours) <- c(
 # 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"
     ) +
@@ -248,15 +248,21 @@ gp <- ggplot() +
         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
     ) +
     annotate(
         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
     )
@@ -279,6 +285,34 @@ if (upside_down == TRUE) {
     )
 }
 
+# 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,

diff --git a/tools/plot_ragtag_paf/plot_ragtag_paf.Rproj b/tools/plot_ragtag_paf/plot_ragtag_paf.Rproj
diff --git a/tools/plot_ragtag_paf/plot_ragtag_paf.xml b/tools/plot_ragtag_paf/plot_ragtag_paf.xml
@@ -42,6 +42,8 @@
             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>
@@ -54,6 +56,8 @@
             <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"/>
         </section>
@@ -81,6 +85,18 @@
                 </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>
     </tests>
     <help>
         Accepts the PAF and AGP produced by the RagTag Scaffold and draws a plot