Merge pull request #145 from TomHarrop/plot_ragtag_v004

Plot ragtag v004
usegalaxy-au · Oct 20, 2024 · 950dfdf · 950dfdf
2 parents b97d17e + b5154b9
commit 950dfdf
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Showing 2 changed files with 18 additions and 5 deletions.
diff --git a/tools/plot_ragtag_paf/plot_ragtag_paf.R b/tools/plot_ragtag_paf/plot_ragtag_paf.R
@@ -253,7 +253,9 @@ gp <- ggplot() +
             q_y + (y_axis_space / 3)
         ),
         hjust = 0.5,
-        vjust = 0.5
+        vjust = 0.5,
+        size = fontsize,
+        size.unit = "pt"
     ) +
     annotate(
         geom = "text",
@@ -264,7 +266,9 @@ gp <- ggplot() +
             t_y - (y_axis_space / 3)
         ),
         hjust = 0.5,
-        vjust = 0.5
+        vjust = 0.5,
+        size = fontsize,
+        size.unit = "pt"
     )
 
 # Reverse the scales and the limits to plot reference on top
@@ -285,6 +289,8 @@ if (upside_down == TRUE) {
     )
 }
 
+
+
 # reference contig names
 if (label_ref_contigs == TRUE) {
     gp <- gp + geom_text(
@@ -295,7 +301,9 @@ if (label_ref_contigs == TRUE) {
             label = tname
         ),
         angle = 30,
-        hjust = ifelse(upside_down == TRUE, 0, 1)
+        hjust = ifelse(upside_down == TRUE, 0, 1),
+        size = 2 * fontsize / 3,
+        size.unit = "pt"
     )
 }
 
@@ -310,6 +318,8 @@ if (label_query_contigs == TRUE) {
         ),
         angle = 30,
         hjust = ifelse(upside_down == TRUE, 1, 0),
+        size = 2 * fontsize / 3,
+        size.unit = "pt"
     )
 }
 

diff --git a/tools/plot_ragtag_paf/plot_ragtag_paf.xml b/tools/plot_ragtag_paf/plot_ragtag_paf.xml
@@ -1,4 +1,4 @@
-<tool id="plot_ragtag_paf" name="Plot RagTag output" version="0.0.3" profile="24.1" license="MIT">
+<tool id="plot_ragtag_paf" name="Plot RagTag output" version="0.0.4" 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>
@@ -103,8 +103,11 @@
         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
+        .. figure:: https://raw.githubusercontent.com/usegalaxy-au/tools-au/refs/heads/master/tools/plot_ragtag_paf/static/images/ragtag.png
            :alt: RagTag plot
+           :width: 600px
+           :height: 400px
+           :align: center
 
     </help>
     <citations>