added missing point_size argument to plotOutliersPDF

MicTott · Mar 27, 2024 · c0f7e9a · c0f7e9a
1 parent 6325c9e
commit c0f7e9a
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Showing 4 changed files with 5 additions and 9 deletions.
diff --git a/R/plotOutliers.R b/R/plotOutliers.R
@@ -33,7 +33,7 @@
 
 plotOutliers <- function(spe, sample_id = "sample_id",
                         sample=unique(spe$sample_id)[1], metric="detected",
-                        outliers=NULL, point_size=1,
+                        outliers=NULL, point_size=2,
                         colors=c("white","black"), stroke=1) {
 
 
@@ -46,7 +46,7 @@ plotOutliers <- function(spe, sample_id = "sample_id",
 
   # Conditionally add outliers if they are not NULL
   if (!is.null(outliers)) {
-    p <- p |> add_ground(var = outliers, stroke = stroke)
+    p <- p |> add_ground(var = outliers, stroke = stroke, point_size = point_size)
   }
 
   # Add title to the plot

diff --git a/R/plotOutliersPDF.R b/R/plotOutliersPDF.R
@@ -34,7 +34,7 @@
 #' @export
 plotOutliersPDF <- function(spe, sample_id="sample_id", metric="detected",
                             outliers="local_outliers",colors=c("white", "black"),
-                            stroke=1, width=5, height=5,fname
+                            stroke=1, point_size=2, width=5, height=5,fname
                             ) {
 
   # Get a list of unique sample IDs
@@ -50,7 +50,8 @@ plotOutliersPDF <- function(spe, sample_id="sample_id", metric="detected",
                     metric=metric,
                     outliers=outliers,
                     colors=colors,
-                    stroke=stroke
+                    stroke=stroke,
+                    point_size=point_size
                     )
 
     # print

diff --git a/README.md b/README.md
@@ -187,11 +187,6 @@ spe <- findArtifacts(spe,
                      n_rings=5,
                      name="artifact"
                     )
-#> [1] "k6"
-#> [1] "k18"
-#> [1] "k36"
-#> [1] "k60"
-#> [1] "k90"
 
 # check that "artifact" is now in colData
 colnames(colData(spe))

diff --git a/man/figures/README-artifact_visualization-1.png b/man/figures/README-artifact_visualization-1.png