plotMarkerMap: Plot ratio of observed to expected counts on reduced...

Description Usage Arguments Value

View source: R/plotFunctions.R

Description

Given some reduced dimensional representation of the data (such as UMAP or tSNE) that has been calculated however you would like, this provides a way to visualise how likely a set of genes are to be soup derived on that map. That is, given a set of genes, this function calculates how many counts would be expected if that droplet were nothing but soup and compares that to the observed count. This is done via a log2 ratio of the two values. A Poisson test is performed and points that have a statistically significant enrichment over the background (at 1

Usage

1
plotMarkerMap(scl, geneSet, DR, ratLims = c(-2, 2))

Arguments

scl

SoupChannelList object.

geneSet

A vector with the names of the genes to aggregate and plot evidence for.

DR

A data.frame, with rows named by unique cell IDs (i.e., <ChannelName>___<Barcode>) the first two columns of which give the coordinates of each cell in some reduced dimension representation of the data.

ratLims

Truncate log ratios at these values.

Value

A ggplot2 containing the plot.


constantAmateur/SoupX documentation built on July 23, 2018, 9:20 a.m.