plotBiomarker {singleCellTK} | R Documentation |
Given a set of genes, return a ggplot of expression values.
plotBiomarker(inSCE, gene, binary = "Binary", visual = "PCA", shape = "No Shape", x = "PC1", y = "PC2", useAssay = "counts", reducedDimName = "PCA")
inSCE |
Input SCtkExperiment object. Required |
gene |
genelist to run the method on. |
binary |
binary/continuous color for the expression. |
visual |
Type of visualization (PCA, tSNE or UMAP). Default: "PCA" |
shape |
shape parameter for the ggplot. |
x |
x coordinate for PCA |
y |
y coordinate for PCA |
useAssay |
Indicate which assay to use. The default is "logcounts". |
reducedDimName |
a name to store the results of the dimension reduction coordinates obtained from this method. This is stored in the SingleCellExperiment object in the reducedDims slot. Required. |
A Biomarker plot
data("mouseBrainSubsetSCE") plotBiomarker(mouseBrainSubsetSCE, gene="C1qa", shape="level1class")