Merge pull request #764 from Ashastry2/master

Updates to plotSCEHeatmap

DESCRIPTION

@@ -62,6 +62,7 @@ Imports:
     ggrepel,
     ggtree,
     gridExtra,
+    grid,
     GSVA (>= 1.50.0),
     GSVAdata,
     igraph,
@@ -85,6 +86,7 @@ Imports:
     shiny,
     shinyjs,
     SingleR,
+    stringr,
     SoupX,
     sva,
     reshape2,
@@ -98,6 +100,7 @@ Imports:
     reticulate (>= 1.14),
     tools,
     tximport,
+    tidyr,
     eds,
     withr,
     GSEABase,
@@ -128,7 +131,6 @@ Suggests:
     lintr,
     spelling,
     org.Mm.eg.db,
-    stringr,
     kableExtra,
     shinythemes,
     shinyBS,

NAMESPACE

@@ -293,8 +293,16 @@ importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,arrange)
+importFrom(dplyr,count)
+importFrom(dplyr,desc)
 importFrom(dplyr,group_by)
+importFrom(dplyr,mutate)
+importFrom(dplyr,one_of)
+importFrom(dplyr,select)
 importFrom(dplyr,summarize)
+importFrom(dplyr,ungroup)
+importFrom(grid,gpar)
 importFrom(magrittr,"%>%")
 importFrom(methods,slot)
 importFrom(reshape2,melt)
@@ -305,7 +313,12 @@ importFrom(rlang,.data)
 importFrom(scuttle,aggregateAcrossCells)
 importFrom(scuttle,aggregateAcrossFeatures)
 importFrom(stats,filter)
+importFrom(stats,prcomp)
+importFrom(stats,quantile)
+importFrom(stringr,str_c)
+importFrom(stringr,str_replace_all)
 importFrom(tibble,tibble)
+importFrom(tidyr,spread)
 importFrom(tools,file_ext)
 importFrom(utils,head)
 importFrom(utils,packageVersion)

R/plotFindMarkerHeatmap.R

@@ -234,9 +234,7 @@ plotFindMarkerHeatmap <- function(inSCE, orderBy = 'size',
                        featureAnnotations = featureAnnotations,
                        cellAnnotations = cellAnnotations,
                        featureAnnotationColor = featureAnnotationColor,
-                       cellAnnotationColor = cellAnnotationColor,
-                       cluster_row_slices = FALSE, rowLabel = rowLabel,
-                       cluster_column_slices = FALSE,
+                       cellAnnotationColor = cellAnnotationColor, rowLabel = rowLabel,
                        rowDend = rowDend, colDend = colDend, title = title, ...)
   return(hm)
 }