chr2plot -> plotChros

progenetix · Oct 19, 2023 · 40a6119 · 40a6119
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diff --git a/docs/file-formats.md b/docs/file-formats.md
@@ -50,7 +50,7 @@ An excerpt of the segment file would look like below:
 #meta=>biosample_count=78
 #plotpars=>title="Testing Custom Plot Parameters"
 #plotpars=>subtitle="Some Chromosomes, Colors etc."
-#plotpars=>chr2plot="3,5,7,8,11,13,16"
+#plotpars=>plotChros="3,5,7,8,11,13,16"
 #plotpars=>color_var_dup_hex=#EE4500;color_var_del_hex=#09F911
 #plotpars=>size_title_left_px=300
 #plotpars=>size_text_title_left_px=10

diff --git a/docs/news/2023-03-09-plotting-docs.md b/docs/news/2023-03-09-plotting-docs.md
@@ -14,7 +14,7 @@ information (though you still will find examples e.g. on the [`use-cases`](/use-
 !!! warn "Plot parameters lost the `-` prefix"
 
     We have removed the `-` prefix from the plot parameter names; e.g. the previous
-    `-chr2plot` selector is now simply `chr2plot`. 
+    `-plotChros` selector is now simply `plotChros`. 
 
 <!--more-->
 

diff --git a/docs/plotting.md b/docs/plotting.md
@@ -38,21 +38,21 @@ Please **use option 1** if accessing complete entities (i.e. only using a single
 #### Examples
 
 * customized plot for glioblastoma CNV frequencies, limited to chromosomes 7, 9 and 10
-    - `progenetix.org/services/collationPlots/?id=NCIT:C3058&chr2plot=7,9,10&colorschema=redgreen&size_plotimage_w_px=640`
+    - `progenetix.org/services/collationPlots/?id=NCIT:C3058&plotChros=7,9,10&colorschema=redgreen&size_plotimage_w_px=640`
 
-![](http://progenetix.org/services/collationPlots/?id=NCIT:C3058&chr2plot=7,9,10&colorschema=redgreen&size_plotimage_w_px=640)
+![](http://progenetix.org/services/collationPlots/?id=NCIT:C3058&plotChros=7,9,10&colorschema=redgreen&size_plotimage_w_px=640)
 
 ## Additional plot parameters
 
 Plot parameters can be added to the request using a standard `&__parameter__=__value__`
 syntax.
 
-* `chr2plot`
+* `plotChros`
     - comma-concatenated list of chromosomes to plot
     - default is 1 -> 22 since X & Y are not always correctly normalized for CNV
   frequencies
-        *  `chr2plot=1,2,3,44,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y`
-        *  `chr2plot=9`
+        *  `plotChros=1,2,3,44,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y`
+        *  `plotChros=9`
 * `size_plotimage_w_px`
     - modifies the width of the plot image in px (default 800)
     - <http://progenetix.org/services/collationPlots/?id=PMID:22824167&size_plotimage_w_px=1084>
@@ -70,8 +70,8 @@ syntax.
     - format is `chro` `:` `start` `-` `end` `:` `some text`
     - multiple labels can be concatenated by `,`
     - colors are randomized from a "decent" palette
-    - <http://progenetix.org/services/collationPlots/?id=pgx:icdom-80123&value_plot_y_max=80&chr2plot=5,8&labels=5:0-48000000:Frequent+5p+gain,8:127735434-127742951:MYC&marker_text_px=12>
-    ![](http://progenetix.org/services/collationPlots/?id=pgx:icdom-80123&value_plot_y_max=80&chr2plot=5,8&labels=5:0-48000000:Frequent+5p+gain,8:127735434-127742951:MYC&marker_text_px=12)
+    - <http://progenetix.org/services/collationPlots/?id=pgx:icdom-80123&value_plot_y_max=80&plotChros=5,8&labels=5:0-48000000:Frequent+5p+gain,8:127735434-127742951:MYC&marker_text_px=12>
+    ![](http://progenetix.org/services/collationPlots/?id=pgx:icdom-80123&value_plot_y_max=80&plotChros=5,8&labels=5:0-48000000:Frequent+5p+gain,8:127735434-127742951:MYC&marker_text_px=12)
 * `marker_text_px`
     - text size for the labels (default 10)
 * `marker_opacity`
@@ -86,8 +86,8 @@ syntax.
         *  `greenred`
         *  `bluered`
 
-    - <http://progenetix.org/services/collationPlots/?id=NCIT:C7376&size_plotarea_h_px=40&value_plot_y_max=50&colorschema=bluered&chr2plot=1,3,9,17,22>
-![](http://progenetix.org/services/collationPlots/?id=NCIT:C7376&size_plotarea_h_px=40&value_plot_y_max=50&colorschema=bluered&chr2plot=1,3,9,17,22)
+    - <http://progenetix.org/services/collationPlots/?id=NCIT:C7376&size_plotarea_h_px=40&value_plot_y_max=50&colorschema=bluered&plotChros=1,3,9,17,22>
+![](http://progenetix.org/services/collationPlots/?id=NCIT:C7376&size_plotarea_h_px=40&value_plot_y_max=50&colorschema=bluered&plotChros=1,3,9,17,22)
 
 
 

diff --git a/docs/use-cases.md b/docs/use-cases.md
@@ -55,7 +55,7 @@ external project such as TCGA
 
 This data can be accessed through the Progenetix API in data and image format.
 
-![Example CNV histogram with custom parameters](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?id=NCIT:C7376&-size_plotarea_h_px=40&-value_plot_y_max=50&-colorschema=bluered&chr2plot=1,3,9,17,22)
+![Example CNV histogram with custom parameters](http://progenetix.org/cgi/PGX/cgi/collationPlots.cgi?id=NCIT:C7376&-size_plotarea_h_px=40&-value_plot_y_max=50&-colorschema=bluered&plotChros=1,3,9,17,22)
 
 Interval frequencies are per default stored in a 1Mb binned format. More
 information about the API use can be found [in the IntervalFrequencies API documentation](services.md#pgxseg-segment-cnv-frequencies).

diff --git a/src/hooks/api.js b/src/hooks/api.js
@@ -338,15 +338,15 @@ export function useCytomapper(querytext) {
   return useProgenetixApi(url)
 }
 
-export function useSubsethistogram({ datasetIds, id, filter, plotRegionLabels, plotGeneSymbols, plotCytoregionLabels, size, chr2plot }) {
+export function useSubsethistogram({ datasetIds, id, filter, plotRegionLabels, plotGeneSymbols, plotCytoregionLabels, size, plotChros }) {
   const svgbaseurl = subsetHistoBaseLink(id, datasetIds)
   const params = []
   filter && params.push(["filter", filter])
   plotRegionLabels && params.push(["plotRegionLabels", plotRegionLabels])
   plotGeneSymbols && params.push(["plotGeneSymbols", plotGeneSymbols])
   plotCytoregionLabels && params.push(["plotCytoregionLabels", plotCytoregionLabels])
   size && params.push(["plotWidth", size])
-  chr2plot && params.push(["chr2plot", chr2plot])
+  plotChros && params.push(["plotChros", plotChros])
   const searchQuery = new URLSearchParams(params).toString()
   return useExtendedSWR(size > 0 && `${svgbaseurl}&${searchQuery}`, svgFetcher)
 }

diff --git a/src/modules/service-pages/dataVisualizationPage.js b/src/modules/service-pages/dataVisualizationPage.js
@@ -135,7 +135,7 @@ function DataVisualizationForm({ isQuerying, sampleCount, onSubmit }) {
       <div className="columns">
         <div className="column">
           <InputField
-            name="chr2plot"
+            name="plotChros"
             label="Chromosomes"
             infoText="The chromosomes to be included in the plot, in the order they should appear. The values should just be the comma-separated chromosome numbers (e.g. '1,3,19,X' - unquoted, no spaces). The default is chr 1-22."
             errors={errors}