plotdiffgenesnb: Function for plotting differentially expressed genes

In dgrun/FateID: Quantification of Fate Bias in Multipotent Progenitors

Function for plotting differentially expressed genes

Description

This is a plotting function for visualizing the output of the diffexpnb function as MA plot.

Usage

plotdiffgenesnb(
  x,
  pthr = 0.05,
  padj = TRUE,
  lthr = 0,
  mthr = -Inf,
  Aname = NULL,
  Bname = NULL,
  show_names = TRUE,
  ...
)

Arguments

x	output of the function diffexpnb.
pthr	real number between 0 and 1. This number represents the p-value cutoff applied for displaying differentially expressed genes. Default value is 0.05. The parameter padj (see below) determines if this cutoff is applied to the uncorrected p-value or to the Benjamini-Hochberg corrected false discovery rate.
padj	logical value. If TRUE, then genes with a Benjamini-Hochberg corrected false discovery rate lower than pthr are displayed. If FALSE, then genes with a p-value lower than pthr are displayed.
lthr	real number between 0 and Inf. Differentially expressed genes are displayed only for log2 fold-changes greater than lthr. Default value is 0.
mthr	real number between -Inf and Inf. Differentially expressed genes are displayed only for log2 mean expression greater than mthr. Default value is -Inf.
Aname	name of expression set A, which was used as input to diffexpnb. If provided, this name is used in the axis labels. Default value is NULL.
Bname	name of expression set B, which was used as input to diffexpnb. If provided, this name is used in the axis labels. Default value is NULL.
show_names	logical value. If TRUE then gene names displayed for differentially expressed genes. Default value is FALSE.
...	Additional arguments for function plot.

Value

None

Examples

x <- intestine$x
y <- intestine$y
v <- intestine$v

tar <- c(6,9,13)
fb <- fateBias(x,y,tar,z=NULL,minnr=5,minnrh=10,nbfactor=5,use.dist=FALSE,seed=NULL,nbtree=NULL)

thr <- .3

A <- rownames(fb$probs)[fb$probs[,"t6"]  > .3]
B <- rownames(fb$probs)[fb$probs[,"t13"] > .3]
de <- diffexpnb(v,A=A,B=B)
plotdiffgenesnb(de,pthr=.05)

dgrun/FateID documentation built on June 20, 2022, 12:57 p.m.