monocle (version 1.6.2)

plot_genes_in_pseudotime: Plots expression for one or more genes as a function of pseudotime

Description

Plots expression for one or more genes as a function of pseudotime

Usage

plot_genes_in_pseudotime(cds_subset, min_expr = NULL, cell_size = 0.75,
  nrow = NULL, ncol = 1, panel_order = NULL, color_by = "State",
  trend_formula = "adjusted_expression ~ sm.ns(Pseudotime, df=3)",
  label_by_short_name = TRUE)

Arguments

cds_subset

CellDataSet for the experiment

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

trend_formula

the model formula to be used for fitting the expression trend over pseudotime

label_by_short_name

label figure panels by gene_short_name (TRUE) or feature id (FALSE)

Value

• a ggplot2 plot object

Examples

data(HSMM)
my_genes <- row.names(subset(fData(HSMM), gene_short_name %in% c("CDK1", "MEF2C", "MYH3")))
cds_subset <- HSMM[my_genes,]
plot_genes_in_pseudotime(cds_subset, color_by="Time")