plotExpression: Plot gene expression along pseudotime.

In koenvandenberge/traviz: Trajectory functions for visualization and interpretation.

Plot gene expression along pseudotime.

Description

Plot gene expression along pseudotime.

Plots a fast loess smoother of gene expression for each lineage.

Usage

plotExpression(counts, sds, gene, ...)

## S4 method for signature 'matrix,SlingshotDataSet,character'
plotExpression(
  counts,
  sds,
  gene,
  type = "loess",
  span = 0.75,
  alpha = 1,
  lwd = 1,
  size = 2/3
)

## S4 method for signature 'matrix,PseudotimeOrdering,character'
plotExpression(
  counts,
  sds,
  gene,
  type = "loess",
  span = 0.75,
  alpha = 1,
  lwd = 1,
  size = 2/3
)

Arguments

counts	The matrix of gene expression counts.
sds	A SlingshotDataSet or PseudotimeOrdering object, typically obtained after trajectory inference using Slingshot.
gene	Gene name of gene to plot.
...	parameters including:
type	The type of smoother. Defaults to "loess".
span	If type is "loess", the span of the smoother. See loess documentation.
alpha	Numeric between 0 and 1, determines the transparency of data points, see scale_color_viridis_d.
lwd	Line width of the smoother. Passed to geom_line.
size	Character expansion of the data points. Passed to geom_point.

Value

A ggplot object.

Examples

library(ggplot2)
data(crv, package="traviz")
data(counts, package="traviz")
plotExpression(counts = counts, sds=crv, gene=rownames(counts)[1])

koenvandenberge/traviz documentation built on Oct. 30, 2024, 8:27 p.m.