support logtGml #30

RGLab · Dec 9, 2017 · c018cf4 · c018cf4
1 parent d064ea2
commit c018cf4
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Showing 5 changed files with 849 additions and 1 deletion.
diff --git a/R/cytobank2GatingSet.R b/R/cytobank2GatingSet.R
@@ -53,7 +53,7 @@ compare.counts <- function(gs, file, id.vars = c("FCS Filename", "population")){
   #load stats from cytobank
   id.vars <- match.arg(id.vars)
   variable.name <- ifelse(id.vars == "population", "FCS Filename", "population")
-  cytobank_counts <- fread(file, stringsAsFactors = FALSE)
+  cytobank_counts <- fread(file, stringsAsFactors = FALSE, blank.lines.skip = TRUE)
 
   if(id.vars == "population"){
     #modify column name because cytobank always put FCS filename

diff --git a/R/graphGML_methods.R b/R/graphGML_methods.R
@@ -303,6 +303,8 @@ setMethod("getTransformations", signature = c(x = "graphGML"), function(x){
         trans.obj <- asinhtGml2_trans(thisTrans@T, thisTrans@M, thisTrans@A)
       }else if(extends(trans.type, "logicletGml2")){
         trans.obj <- logicleGml2_trans(thisTrans@T, thisTrans@M, thisTrans@W, thisTrans@A)
+      }else if(extends(trans.type, "logtGml2")){
+        trans.obj <- logtGml2_trans(thisTrans@T, thisTrans@M)
       }else
         stop("Don't know how to inverse transformation: ", trans.type)
 

diff --git a/inst/extdata/cytotrol_tcell_cytobank_logt_counts.csv b/inst/extdata/cytotrol_tcell_cytobank_logt_counts.csv
@@ -0,0 +1,6 @@
+FCS Filename,CytoTrol_CytoTrol_1.fcs
+cd3_EventCounts,56392
+tsubUR_EventCounts,896
+tsubUL_EventCounts,16721
+tsubLL_EventCounts,2485
+tsubLR_EventCounts,36290