fix gene_pheatmap not working for some data

jminnier · Oct 14, 2020 · e82ead2 · e82ead2
1 parent 6353cc6
commit e82ead2
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Showing 2 changed files with 9 additions and 1 deletion.
diff --git a/fun-groupplots.R b/fun-groupplots.R
@@ -19,7 +19,7 @@
 ## ==================================================================================== ##
 ## 
 gene_pheatmap <- function(data_long,valuename,sampleid,annotation_row=NULL) {
-  data_long$value = data_long[,valuename]
+  data_long <- data_long %>% mutate(value=unlist(data_long[,valuename]))
   exprdat = data_long%>%select(unique_id,sampleid,value)%>%spread(sampleid,value)
   exprdat = as.matrix(exprdat[,-1])
 

diff --git a/tests.R b/tests.R
@@ -28,6 +28,9 @@ glimpse(tmp3$results)
 tmp3 <- analyze_expression_data(testdata, analysis_method="linear_model", numgeneids = 2)
 glimpse(tmp3$data_long)
 glimpse(tmp3$results)
+gene_pheatmap(data_long = tmp3$data_long,
+              sampleid = tmp3$sampledata$sampleid,
+              valuename = "log2cpm")
 
 # non-counts
 testdata  <- read_csv("data/testdata_noncounts.csv")
@@ -55,6 +58,11 @@ rna_scatterplot(data_long = tmp4$data_long,
                 color_hi = "orange",
                 sel_genes = NULL
 )
+gene_pheatmap(data_long = tmp4$data_long,
+              sampleid = tmp4$sampledata$sampleid,
+              valuename = "log2cpm")
+
+
 png("tmp.png") # can't render in rstudio at the moment
 heatmap_render(
   data_analyzed=tmp4,