Fixed data preprocessing bugs. v0.2.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: scClustViz
 Type: Package
 Title: Differential Expression-based scRNAseq Cluster Assessment and Viewing
-Version: 0.2.2
+Version: 0.2.3
 Date: 2018-08-21
 Authors@R: c(as.person("Brendan T. Innes <brendan.innes@mail.utoronto.ca> [aut,cre]"),
              as.person("Gary D. Bader [aut,ths]"))

NAMESPACE

@@ -1,10 +1,10 @@
-# Generated by roxygen2: do not edit by hand
-
-export(clusterWiseDEtest)
-export(meanLogX)
-export(readFromManual)
-export(readFromSeurat)
-export(runShiny)
-import(shiny)
-importFrom(scales,alpha)
-importFrom(viridis,viridis)
+# Generated by roxygen2: do not edit by hand
+
+export(clusterWiseDEtest)
+export(meanLogX)
+export(readFromManual)
+export(readFromSeurat)
+export(runShiny)
+import(shiny)
+importFrom(scales,alpha)
+importFrom(viridis,viridis)

R/deTest.R

@@ -230,8 +230,10 @@ clusterWiseDEtest <- function(il,testAll=TRUE,
     deM_dDR <- apply(combos,2,function(i) DR[i[1],] - DR[i[2],])
     deM_logGER <- apply(combos,2,function(i) MTC[i[1],] - MTC[i[2],])
     deM_genesUsed <- switch(threshType,
-                            dDR=apply(deM_dDR,2,function(X) which(abs(X) > dDRthresh)),
-                            logGER=apply(deM_logGER,2,function(X) which(abs(X) > logGERthresh))) 
+                            dDR=sapply(colnames(combos),function(X) 
+                              which(abs(deM_dDR[,X]) > dDRthresh),simplify=F),
+                            logGER=sapply(colnames(combos),function(X) 
+                              which(abs(deM_logGER[,X]) > logGERthresh),simplify=F)) 
     if (any(sapply(deM_genesUsed,length) < 1)) {
       stop("Gene filtering threshold is set too high.")
     }

R/importData.R

@@ -76,13 +76,16 @@ readFromSeurat <- function(inD) {
   out <- list()
   out[["nge"]] <- inD@data
 
-  out[["md"]] <- inD@meta.data[,!grepl("res\\.[0-9]",colnames(inD@meta.data))]  
+  out[["md"]] <- inD@meta.data[,!grepl("res\\.[0-9]",colnames(inD@meta.data))]
+  for (X in which(sapply(out[["md"]],is.character))) {
+    out[["md"]][[X]] <- as.factor(out[["md"]][[X]])
+  }
   # metadata for cells (dataframe of cells), not including cluster assignments.
 
   if (is.data.frame(inD@meta.data[,grepl("res\\.[0-9]",colnames(inD@meta.data))])) {
     cl <- data.frame(lapply(inD@meta.data[,grepl("res\\.[0-9]",colnames(inD@meta.data))],as.factor))
   } else {
-    cl <- data.frame(inD@meta.data[,grepl("res\\.[0-9]",colnames(inD@meta.data))])
+    cl <- data.frame(inD@meta.data[,grepl("res\\.[0-9]",colnames(inD@meta.data))],stringsAsFactors=T)
     colnames(cl) <- grep("res\\.[0-9]",colnames(inD@meta.data),value=T)
   }
   rownames(cl) <- rownames(inD@meta.data) 
@@ -177,6 +180,9 @@ readFromManual <- function(nge,md,cl,dr_clust,dr_viz) {
   out <- list()
   out[["nge"]] <- nge
   out[["md"]] <- md
+  for (X in which(sapply(out[["md"]],is.character))) {
+    out[["md"]][[X]] <- as.factor(out[["md"]][[X]])
+  }
   if (!all(sapply(cl,is.factor))) {
     temp_cells <- rownames(cl)
     cl <- data.frame(lapply(cl,as.factor))