Given a set of genes, return a ggplot of expression values.
plotBiomarker( inSCE, gene, binary = "Binary", shape = "No Shape", useAssay = "counts", reducedDimName = "PCA", x = NULL, y = NULL, comp1 = NULL, comp2 = NULL )
Input SCtkExperiment object. Required
genelist to run the method on.
binary/continuous color for the expression.
shape parameter for the ggplot.
Indicate which assay to use. The default is "logcounts".
results name of dimension reduction coordinates obtained from this method. This is stored in the SingleCellExperiment object in the reducedDims slot. Required.
PCA component to be used for plotting(if applicable). Default is first PCA component for PCA data and NULL otherwise.
PCA component to be used for plotting(if applicable). Default is second PCA component for PCA data and NULL otherwise.
label for x-axis
label for y-axis
A Biomarker plot
data("mouseBrainSubsetSCE") plotBiomarker(mouseBrainSubsetSCE, gene="C1qa", shape="level1class", reducedDimName="TSNE_counts")