plotScase: Main function for plotting ASE fits in single-cell data

In lulizou/spASE: Detecting Allele-Specific Expression in Spatial Transcriptomics

Main function for plotting ASE fits in single-cell data

Description

This function plots stuff for scase results.

Usage

plotScase(
  matrix1,
  matrix2,
  scasefit,
  genes = NULL,
  save = NULL,
  breaks = c(1, 2, 5, 10, 50, 100, 250, 500, 1000, 2000)
)

Arguments

matrix1	a matrix of counts where the rows are genes and the columns are cells for allele 1. This one is the one that gets its probability modeled. Must have row names and column names to identify genes and cells.
matrix2	a matrix of counts where the rows are genes and the columns are cells for allele 2.
scasefit	the resulting data frame from a call to scase
genes	a vector of genes given as strings to plot. default is NULL which will plot the first gene in the scasefit results dataframe.
save	the filename prefix to save if want to save instead of visualize. Default is null meaning no file will be saved.
breaks	how to split up the total UMI counts for coloring. there is a default setting which should work for most data sets.

Details

Takes in the result from scase and plots desired genes with beta distribution overlaid on the histogram of allele1 proportion, confidence interval plot for the desired genes, and the overall distribution of p and phi for all genes

Value

Multiple ggplot2 plots or, instead, each one gets saved to a different file starting with the prefix defined in the save parameter.

lulizou/spASE documentation built on May 22, 2024, 5:24 a.m.