@@ -129,7 +129,7 @@ mergeMatricesForPlotCOMPASSResultStack <- function(x,

   catsMerged <- catsMerged[order(catsMerged$Counts),]

   # Make all columns a factor, except for `name`

   catsMergedRowNamesTmp <- catsMerged$name

-  catsMerged <- as.data.frame(sapply(catsMerged, as.factor))

+  catsMerged <- as.data.frame(sapply(catsMerged, as.factor), stringsAsFactors=TRUE)

   catsMerged$name <- catsMergedRowNamesTmp # not a factor

   rownames(catsMerged) <- catsMerged$name

@@ -196,7 +196,7 @@ test_that("mergeMatricesForPlotCOMPASSResultStack merges mean_gamma matrices cor

                          "Seed2" = cr5,

                          "Seed3" = cr6)

-  mergedMatrices <- COMPASS:::mergeMatricesForPlotCOMPASSResultStack(compassResults,

+  mergedMatrices <- mergeMatricesForPlotCOMPASSResultStack(compassResults,

                                                            row_annotation = c("Seed"),

                                                            variable = "Seed")

@@ -5,7 +5,9 @@ gs <- load_gs(dataDir)

 gs1 <- gs_clone(gs)

 gs2 <- gs_clone(gs)

 sampleNames(gs2) <- "sample2.fcs"

-gs <- merge_list_to_gs(GatingSetList(list(gs1, gs2)))

+gs <- merge_list_to_gs(list(gs1, gs2))

+cs <- gs_cyto_data(gs)

+cs_lock(cs)#make sure compass code doesn't modify cs/cf object in place

 pd <- pData(gs)

 pd[["name"]] <- rownames(pd)

 pd[["PTID"]] <- 1