check that clone genome plot works when filename = NULL and remove /d…

…ontrun in .Rd file
uclahs-cds · Nov 4, 2024 · 5f7c7a4 · 5f7c7a4
1 parent 29c0fb2
commit 5f7c7a4
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Showing 2 changed files with 3 additions and 5 deletions.
diff --git a/R/create.clone.genome.distribution.plot.R b/R/create.clone.genome.distribution.plot.R
@@ -100,7 +100,7 @@ create.clone.genome.distribution.plot.per.sample <- function(
     # calculate densities for each cluster --------------------------------------------------------
     density.list <- list();
     for (k in unique(sample.df$clone.id)) {
-        if (sum(sample.df$clone.id == k) <= 1) {
+        if (sum(sample.df$clone.id == k, na.rm = TRUE) <= 1) {
             warning(paste('Skipping clone', k, 'in sample', unique(sample.df$ID), 'since there is only one SNV'));
             next;
         }

diff --git a/man/create.clone.genome.distribution.plot.Rd b/man/create.clone.genome.distribution.plot.Rd
@@ -41,8 +41,6 @@ This function preprocesses the input data frame, extracts chromosome information
 setseed(123);
 load(file.path(system.file('data', package = 'CancerEvolutionVisualization'), 'SNV.Rda'));
 
-\dontrun{create.clone.genome.distribution.plot(
-    snv,
-    filename = './clone-genome-dist-plot.png'
-    )};
+create.clone.genome.distribution.plot(snv);
+
 }