View source: R/Script_PLATE_10_ADHOC_PLOT_2_PlotValues_Gene.R
PlotValues.Exp | R Documentation |
Boxplot of gene expression values across different groups of cells.
PlotValues.Exp( MarvelObject, cell.group.list, feature, maintitle = "gene_short_name", xlabels.size = 8, cell.group.colors = NULL, point.alpha = 0.2 )
MarvelObject |
Marvel object. S3 object generated from |
cell.group.list |
List of character strings. Each element of the list is a vector of cell IDs corresponding to a cell group. The name of the element will be the cell group label. |
feature |
Character string. |
maintitle |
Character string. Column to use as plot main title as per |
xlabels.size |
Numeric value. Size of x-axis labels as per |
cell.group.colors |
Character string. Vector of colors for the cell groups specified for PCA analysis using |
point.alpha |
Numeric value. Transparency of the data points. Takes any values between 0-1. Default value is |
An object of class S3 with new slot MarvelObject$adhocPlot$Exp
.
marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL")) df.pheno <- marvel.demo$SplicePheno cell.group.g1 <- df.pheno[which(df.pheno$cell.type=="iPSC"), "sample.id"] cell.group.g2 <- df.pheno[which(df.pheno$cell.type=="Endoderm"), "sample.id"] cell.group.list <- list(cell.group.g1, cell.group.g2) names(cell.group.list) <- c("iPSC", "Endoderm") # Plot marvel.demo <- PlotValues.Exp(MarvelObject=marvel.demo, cell.group.list=cell.group.list, feature="ENSG00000161970.15", xlabels.size=8 ) # Check output marvel.demo$adhocPlot$Exp
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