Description Usage Arguments Value Examples
View source: R/plotBiomarker.R
Given a set of genes, return a ggplot of expression values.
1 2 3 4 5 6 7 8 9 10 11 12 | plotBiomarker(
inSCE,
gene,
binary = "Binary",
shape = "No Shape",
useAssay = "counts",
reducedDimName = "PCA",
x = NULL,
y = NULL,
comp1 = NULL,
comp2 = NULL
)
|
inSCE |
Input SingleCellExperiment object. |
gene |
genelist to run the method on. |
binary |
binary/continuous color for the expression. |
shape |
shape parameter for the ggplot. |
useAssay |
Indicate which assay to use. The default is "logcounts". |
reducedDimName |
results name of dimension reduction coordinates obtained from this method. This is stored in the SingleCellExperiment object in the reducedDims slot. Required. |
x |
PCA component to be used for plotting(if applicable). Default is first PCA component for PCA data and NULL otherwise. |
y |
PCA component to be used for plotting(if applicable). Default is second PCA component for PCA data and NULL otherwise. |
comp1 |
label for x-axis |
comp2 |
label for y-axis |
A Biomarker plot
1 2 | data("mouseBrainSubsetSCE")
plotBiomarker(mouseBrainSubsetSCE, gene="C1qa", shape="level1class", reducedDimName="TSNE_counts")
|
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