@@ -7,6 +7,7 @@

 findMarkerDiffExp(

   inSCE,

   useAssay = "logcounts",

+  useReducedDim = NULL,

   method = c("wilcox", "MAST", "DESeq2", "Limma", "ANOVA"),

   cluster = "cluster",

   covariates = NULL,

@@ -23,6 +24,10 @@ findMarkerDiffExp(

 \item{useAssay}{character. A string specifying which assay to use for the

 MAST calculations. Default \code{"logcounts"}.}

+\item{useReducedDim}{character. A string specifying which reducedDim to use

+for MAST calculations. Set \code{useAssay} to \code{NULL} when using. 

+Required.}

+

 \item{method}{A single character for specific differential expression

 analysis method. Choose from \code{'wilcox'}, \code{'MAST'}, \code{'DESeq2'},

 \code{'Limma'}, and \code{'ANOVA'}. Default \code{"wilcox"}.}

@@ -20,7 +20,7 @@ plotMarkerDiffExp(

   cellAnnotations = NULL,

   featureAnnotationColor = NULL,

   cellAnnotationColor = NULL,

-  colSplitBy = ifelse(is.null(orderBy), NULL, colnames(inSCE@metadata$findMarker)[5]),

+  colSplitBy = NULL,

   rowSplitBy = "marker",

   rowDend = FALSE,

   colDend = FALSE,