plotSmoothers {tradeSeq}R Documentation

Plot the log-transformed counts and the fitted values for a particular gene along all lineages

Description

Plot the smoothers estimated by tradeSeq.

Usage

plotSmoothers(models, ...)

## S4 method for signature 'gam'
plotSmoothers(models, nPoints = 100, lwd = 2,
  size = 2/3, xlab = "Pseudotime", ylab = "Log(expression + 1)",
  border = TRUE, alpha = 1)

## S4 method for signature 'SingleCellExperiment'
plotSmoothers(models, counts, gene,
  nPoints = 100, lwd = 2, size = 2/3, xlab = "Pseudotime",
  ylab = "Log(expression + 1)", border = TRUE, alpha = 1)

Arguments

models

Either the SingleCellExperiment object obtained after running fitGAM, or the specific GAM model for the corresponding gene, if working with the list output of tradeSeq.

...

parameters including:

nPoints

The number of points used to extraplolate the fit

lwd

Line width of the smoother. Passed to geom_line

size

Character expansion of the data points. Passed to geom_point

xlab

x-axis label. Passed to labs

ylab

y-axis label. Passed to labs

border

logical: should a white border be drawn around the mean smoother.

alpha

Numeric between 0 and 1, determines the transparancy of data points, see scale_color_viridis_d.

counts

The matrix of gene expression counts.

gene

Gene name of gene to plot.

Value

A ggplot object

Examples

data(gamList, package = "tradeSeq")
plotSmoothers(gamList[[4]])

[Package tradeSeq version 1.0.1 Index]