Plot violin plots for gene expression
Generates violin plots of expression of specified gene for each dataset.
plotGeneViolin( object, gene, methylation.indices = NULL, by.dataset = TRUE, return.plots = FALSE )
object |
|
gene |
Gene for which to plot relative expression. |
methylation.indices |
Indices of datasets in object with methylation data (this data is not magnified and put on log scale). |
by.dataset |
Plots gene expression for each dataset separately (default TRUE). |
return.plots |
Return ggplot objects instead of printing directly to console (default FALSE). |
List of ggplot plot objects (only if return.plots TRUE, otherwise prints plots to console).
## Not run: # ligerex (liger object based on in-memory datasets), factorization complete # plot expression for CD4 and return plots violin_plots <- plotGeneViolin(ligerex, "CD4", return.plots = TRUE) # ligerex (liger object based on datasets in HDF5 format), factorization complete input ligerex <- readSubset(ligerex, slot.use = "norm.data", max.cells = 5000) violin_plots <- plotGeneViolin(ligerex, "CD4", return.plots = TRUE) ## End(Not run)
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