Update report.qmd to handle other colours

PGScatalog · Oct 2, 2023 · c4719f4 · c4719f4
1 parent 5276ae8
commit c4719f4
Showing 1 changed file with 19 additions and 8 deletions.
diff --git a/assets/report/report.qmd b/assets/report/report.qmd
@@ -293,12 +293,23 @@ if(params$run_ancestry == TRUE){
 ```{r colour_palette, echo = FALSE, eval=params$run_ancestry}
 # source: https://github.com/PGScatalog/PGS_Catalog/blob/master/catalog/static/catalog/pgs.scss#L2493-L2520
 # $ancestry_colours
-thousand_genomes_colours <- c("#FFD900", "#E41A1C", "#B15928", "#4DAF4A", 
-                              "#377EB8", "#00CED1", "#984EA3", "#A6CEE3", 
-                              "#FF7F00", "#BBB", "#999")
-names(thousand_genomes_colours) <- c("AFR", "AMR", "ASN", "EAS", "EUR", "GME",
-                                     "SAS", "MAE", "MAO", "NR", "OTH")
-thousand_genomes_palette <- scale_colour_manual(name = "Populations", values = thousand_genomes_colours)
+if({params$reference_panel_name} == '1000G'){
+  thousand_genomes_colours <- c("#FFD900", "#E41A1C", "#B15928", "#4DAF4A",
+                                "#377EB8", "#00CED1", "#984EA3", "#A6CEE3",
+                                "#FF7F00", "#BBB", "#999")
+  names(thousand_genomes_colours) <- c("AFR", "AMR", "ASN", "EAS",
+                                       "EUR", "GME", "SAS", "MAE",
+                                       "MAO", "NR", "OTH")
+  current_population_palette <- scale_colour_manual(name = "Populations", values = thousand_genomes_colours)
+} else if({params$reference_panel_name} == 'HGDP+1kGP'){
+  gnomAD_pop_colours <- c("#97519d", "#e42523", "#f67e1e", "#48b24b",
+                          "#3280bb", "#a65528", "#9a9c9b")
+  names(gnomAD_pop_colours) <- c("AFR", "AMR", "CSA", "EAS",
+                                 "EUR", "MID", "OCE")
+  current_population_palette <- scale_colour_manual(name = "Populations", values = gnomAD_pop_colours)
+} else{
+  current_population_palette <- scale_colour_brewer(palette="Set3")
+}
 ```
 
 ```{r, echo = FALSE, message = FALSE, eval=params$run_ancestry}
@@ -321,7 +332,7 @@ for(pc in seq.int(1,5,2)){
   if (pcX %in% colnames(popsim)){
     p_pca <- ggplot(popsim[popsim$REFERENCE == TRUE,], aes(x=!!sym(pcX), y=!!sym(pcY))) + geom_point(aes(colour=SuperPop, shape=slabel), alpha=0.25)
     p_pca <- p_pca + geom_point(data=popsim[popsim$REFERENCE != TRUE,], aes(color=MostSimilarPop, shape=slabel))
-    p_pca <- p_pca + theme_bw() + thousand_genomes_palette + scale_shape_manual(values=map_shapes, name='sampleset')
+    p_pca <- p_pca + theme_bw() + current_population_palette + scale_shape_manual(values=map_shapes, name='sampleset')
     print(p_pca)
   }
 }
@@ -492,4 +503,4 @@ For scores from the PGS Catalog, please remember to cite the original publicatio
 
 > PGS Catalog Calculator (in development). PGS Catalog Team. `https://github.com/PGScatalog/pgsc_calc`
 
-> Lambert et al. (2021) The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics. 53:420–425 doi:10.1038/s41588-021-00783-5.
+> Lambert et al. (2021) The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nature Genetics. 53:420–425 doi:10.1038/s41588-021-00783-5.