plot_accessibility_in_pseudotime: Plot accessibility by pseudotime

In cole-trapnell-lab/cicero: Predict cis-co-accessibility from single-cell chromatin accessibility data

Plot accessibility by pseudotime

Description

Make a barplot of chromatin accessibility across pseudotime

Usage

plot_accessibility_in_pseudotime(cds_subset, breaks = 10)

Arguments

cds_subset	Subset of the CDS object you want to plot. The CDS must have a column in the pData table called "Pseudotime".
breaks	Number of breaks along pseudotime. Controls the coarseness of the plot.

Details

This function plots each site in the CDS subset by cell pseudotime as a barplot. Cells are divided into bins by pseudotime (number determined by breaks) and the percent of cells in each bin that are accessible is represented by bar height. In addition, the black line represents the pseudotime-dependent average accessibility from a smoothed binomial regression.

Value

ggplot object

Examples

## Not run: 
plot_accessibility_in_pseudotime(input_cds_lin[c("chr18_38156577_38158261",
                                                 "chr18_48373358_48374180",
                                                 "chr18_60457956_60459080")])

## End(Not run)

cole-trapnell-lab/cicero documentation built on March 13, 2023, 6:02 p.m.