plot_genes_violin: Plots expression for one or more genes as a violin plot

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Accepts a subset of a CellDataSet and an attribute to group cells by, and produces one or more ggplot2 objects that plots the level of expression for each group of cells.

Usage

plot_genes_violin(cds_subset, grouping = "State", min_expr = NULL,
  cell_size = 0.75, nrow = NULL, ncol = 1, panel_order = NULL,
  color_by = NULL, plot_trend = FALSE, label_by_short_name = TRUE,
  relative_expr = TRUE, log_scale = TRUE)

Arguments

cds_subset	CellDataSet for the experiment
grouping	the cell attribute (e.g. the column of pData(cds)) to group cells by on the horizontal axis
min_expr	the minimum (untransformed) expression level to use in plotted the genes.
cell_size	the size (in points) of each cell used in the plot
nrow	the number of rows used when laying out the panels for each gene's expression
ncol	the number of columns used when laying out the panels for each gene's expression
panel_order	the order in which genes should be layed out (left-to-right, top-to-bottom)
color_by	the cell attribute (e.g. the column of pData(cds)) to be used to color each cell
plot_trend	whether to plot a trendline tracking the average expression across the horizontal axis.
label_by_short_name	label figure panels by gene_short_name (TRUE) or feature id (FALSE)
relative_expr	Whether to transform expression into relative values
log_scale	a boolean that determines whether or not to scale data logarithmically

Value

a ggplot2 plot object

Examples

## Not run: 
library(HSMMSingleCell)
HSMM <- load_HSMM()
my_genes <- HSMM[row.names(subset(fData(HSMM), gene_short_name %in% c("ACTA1", "ID1", "CCNB2"))),]
plot_genes_violin(my_genes, grouping="Hours", ncol=2, min_expr=0.1)

## End(Not run)

monocle documentation built on Nov. 8, 2020, 5:06 p.m.