minor updates

HuntsmanCancerInstitute · Jan 22, 2025 · b198e04 · b198e04
1 parent 14a791c
commit b198e04
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/R/plot_fgsea.R b/R/plot_fgsea.R
@@ -32,7 +32,7 @@ plot_fgsea <- function(x, trim=70, sets, nes=TRUE, cluster_row=FALSE,  cluster_c
    z <- dplyr::select(y, contrast, pathway, NES) %>%
          tidyr::spread(contrast, NES)
    }else{
-   z <- dplyr::select(y, contrast, pathway, ES) %>%
+   z <- dplyr::select(y, contrast, pathway, ES) %>% 
          tidyr::spread(contrast, ES)
    }
    if(!missing(sets)){

diff --git a/R/read_featureCounts.R b/R/read_featureCounts.R
@@ -34,6 +34,8 @@ read_featureCounts <- function( path=".", pattern, reshape=TRUE, stats=FALSE){
       fc <- read_sample_files(path, pattern, col_names=c("status", "count"), skip=1)
       if(reshape){
            fc <- dplyr::filter(fc, count!=0) %>% tidyr::spread(status, count)
+           #fix for Autoanalysis
+           fc$sample <- gsub("_Hg38|_GRCm39", "", fc$sample )
            #  add option to sort HCI samples as X1, X2, ..., X10, X11
            fc  <-  fc[ order_samples(fc$sample), ]
       }