plot_compareClusts: scClustViz plot: Volcano and MA-style plots to compare...

In BaderLab/scClustViz: Differential Expression-based scRNAseq Cluster Assessment and Viewing

scClustViz plot: Volcano and MA-style plots to compare clusters

Description

This function generates scatterplots inspired by volcano and MA plots for comparing gene expression between pairs of clusters.

Usage

plot_compareClusts(
  sCVd,
  clA,
  clB,
  dataType,
  labType = "de",
  labGenes,
  labNum = 5,
  labTypeDiff = "logGER"
)

Arguments

sCVd	The sCVdata object.
clA	Cluster identifier for side A of the comparison.
clB	Cluster identifier for side B of the comparison.
dataType	For MA-style plots comparing difference and mean of gene summary statistics, one of: "DR" (detection rate); "MGE" (mean gene expression); "MDGE" (mean detected gene expression). For volcano plots, the effect size measure can be one of: "dDR" (difference in detection rate); "logGER" (log gene expression ratio). To compare relationship between difference in detection rate and log gene expression ratio, use "GERvDDR".
labType	Default="de". A character vector indicating which genes to highlight. One of "de" (most statistically significant genes), "diff" (most different by dataType shown), or "search" (specified genes).
labGenes	Only required if labType="search". Gene names to highlight.
labNum	Default=5. Number of genes to highlight per side.
labTypeDiff	Default="logGER". Only required if dataType="GERvDDR" and labType="diff". Which axis to use for difference calculation. One of "dDR" (difference in detection rate) or "logGER" (log gene expression ratio).

Examples

## Not run: 
plot_compareClusts(sCVdata,
                   clA="1",
                   clB="2",
                   dataType="GERvDDR",
                   labType="search",
                   labGenes="Actb")

## End(Not run)

BaderLab/scClustViz documentation built on Sept. 10, 2023, 11:51 p.m.