plot_in_pseudotime: Plot cells in pseudotime

In kieranrcampbell/embeddr: Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data

Description

Plot a set of genes through pseudotime using smooth LOESS curves.

Usage

plot_in_pseudotime(sce, nrow = NULL, ncol = NULL, use_short_names = FALSE,
  use_log_scale = FALSE, facet_wrap_scales = "fixed",
  color_by = "cluster", y_lab = "Expression")

Arguments

sce	An object of class SCESet
nrow	Number of rows of plots; passed to facet_wrap
ncol	Number of columns of plots; passed to facet_wrap
use_short_names	Logical If pData(sce) contains a gene_short_name column (such as in the monocle dataset HSMM) then the names in the resulting plot will be the gene short names.
use_log_scale	Logical If TRUE scale_y_log10 is added to plot
facet_wrap_scales	Passed to the scales argument in facet_wrap. Should scales be fixed ('fixed', the default), free ('free'), or free in one dimension ('free_x', 'free_y')
color_by	What variable should points be coloured by? Must be in pData(sce) or NULL
y_lab	Y-axis label for plot.

Value

A ggplot2 plot

Examples

library(scater)
data('sc_example_counts') ; sce <- newSCESet(countData = sc_example_counts)
sce <- embeddr(sce)
sce <- fit_pseudotime(sce)
plot_in_pseudotime(sce[1:4,]) # plot first four genes

kieranrcampbell/embeddr documentation built on May 20, 2019, 9:24 a.m.