Merge pull request #41 from nf-osi/jaybee84/add_genes

issue_40
nf-osi · Apr 12, 2021 · 07c4532 · 07c4532
2 parents 36eb92c + 8ac50b8
commit 07c4532
Show file tree

Hide file tree

Showing 5 changed files with 7 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -35,3 +35,5 @@ Suggests:
 VignetteBuilder: knitr
 URL: https://github.com/allaway/kairos
 BugReports: https://github.com/allaway/kairos/issues
+Depends: 
+    R (>= 2.10)
diff --git a/R/mod_gene_var.R b/R/mod_gene_var.R
@@ -151,8 +151,8 @@ mod_gene_variant_server <- function(input, output, session, specimens){
 
     #Color coding for Annotation
 
-    col1 <- c("#f6511d", "#ffb400", "#00a6ed") #, "#7fb800", "#0d2c54")
-    col2 <- c("#6da34d", "#56445d", "#548687") #, "#8fbc94", "#c5e99b")
+    col1 <- c("#f6511d", "#ffb400", "#00a6ed", "#7fb800", "#0d2c54")
+    col2 <- c("#6da34d", "#56445d", "#548687", "#8fbc94", "#c5e99b")
 
     names(col1) <- as.vector(unique(kairos::jhu_tumor_file@clinical.data$tumorType))
     names(col2) <- as.vector(unique(kairos::jhu_tumor_file@clinical.data$sampleType))

diff --git a/data-raw/jhu_maf.R b/data-raw/jhu_maf.R
@@ -1,3 +1,4 @@
 #Prep Maf file for plotting
-load("data-raw/jhu_maf.RData")
-usethis::use_data(jhu_tumor_file)
+load("data-raw/jhu_maf_updated.RData")
+jhu_tumor_file <- kairos_file
+usethis::use_data(jhu_tumor_file, overwrite = TRUE)
diff --git a/data-raw/jhu_maf_updated.RData b/data-raw/jhu_maf_updated.RData
diff --git a/data/jhu_tumor_file.rda b/data/jhu_tumor_file.rda