blotPlot: Generate violin plots with a high density fit (i.e. blot...

In joeburns06/hocuspocus: A Suite of Single-Cell RNA-Seq Analysis Tools Built for Dummy Biologists

Description

Takes ExpressionSet object and generates blot plots for the specified groups and genes.

Usage

blotPlot(cellData, genes, groups = "GroupID", cols = 1, singleGroup,
  singleColor = "red", order = TRUE, save = FALSE)

Arguments

cellData	ExpressionSet object created with readCells (and preferably transformed with prepCells).
genes	Vector of character strings specifying the names of genes to plot. All gene names must be genes that are present in the expression matrix.
groups	Character string specifying the title of the column in pData that contains the names of the groups to which each sample belongs. The blots representing each group in the plots for each gene will be colored accordingly. The column length should be the same length as the number of samples.
cols	Integer specifying the number of columns in which to arrange the blot plots. The number of cols should be less than or equal to the number of genes.
singleGroup	Character string specifying the name of a single group within groups to plot. Individual blot plots are generated for each gene on a single set of axes.
singleColor	Character string specifying the color to use for the singleGroup blot plot.
order	Boolean specifying whether the groups should be arranged in alphabetical factor order prior to plotting. If FALSE, the current order of levels is used.
save	Boolean specifying whether to save the resultant plot as a .tiff file.

Value

Blot plots for the specified groups and genes in a new window.

joeburns06/hocuspocus documentation built on May 19, 2019, 2:59 p.m.