correct median color pcawg test example

README.md

@@ -6,4 +6,4 @@ repertoire of mutational signatures in human cancer**. *Nature* 2020.
 [doi](https://www.nature.com/articles/s41586-020-1943-3).
 
 An example of the current state of development with this picture.
-<embed src="/tests/testthat/pdfs_plots/extra_table_grob_cols_more_rows_more_with_color.pdf" type="application/pdf">
+![pcawg](assets/table_extra_grob_pcawg.png)

tests/testthat/helper.R

 suppressMessages(library(SummarizedExperiment))
 suppressMessages(library(dplyr))
+suppressMessages(library(tibble))
 
 load("testdata/DBS.rda")
 load("testdata/DEXP.rda")

tests/testthat/test-table_extra_grob.R

@@ -137,7 +137,9 @@ test_that("extra table grob on pcawg works", {
 
   dcolor <- pcawg_counts %>%
     group_by(Cancer.Types) %>%
-    summarize_at(vars(-Sample.Names, -Accuracy), ~median(.x*1e6/3.2e9))
+    summarize_at(vars(-Sample.Names, -Accuracy), ~median(.[.!=0]*1e6/3.2e9)) %>%
+    replace(is.na(.),0)
+
   dcolor <- column_to_rownames(.data=dcolor, var="Cancer.Types")
   dcolor <- t(as.matrix(dcolor))