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

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

Description

Plots expression for one or more genes as a function of pseudotime. Plotting allows you determine if the ordering produced by orderCells() is correct and it does not need to be flipped using the "reverse" flag in orderCells

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 = "~ sm.ns(Pseudotime, df=3)", label_by_short_name = TRUE,
  relative_expr = TRUE, vertical_jitter = NULL, horizontal_jitter = NULL)

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)
relative_expr	Whether to transform expression into relative values
vertical_jitter	A value passed to ggplot to jitter the points in the vertical dimension. Prevents overplotting, and is particularly helpful for rounded transcript count data.
horizontal_jitter	A value passed to ggplot to jitter the points in the horizontal dimension. Prevents overplotting, and is particularly helpful for rounded transcript count data.

Value

a ggplot2 plot object

Examples

## Not run: 
library(HSMMSingleCell)
HSMM <- load_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")

## End(Not run)

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