plotPIrank: PI rank plot

In CenterForStatistics-UGent/PIMseq: PIM for testing differential expression in single cell RNA-seq data

PI rank plot

Description

Plots gene ranking based on the estimated PI. Low-regulated genes (PI <0.5) appear in the left edge and up-regulated genes appear in the right edge. Error bars indicate the (1-alpha)*100 confidence interval estimate of the PI.

Usage

plotPIrank(pim.res, contrast, add.PI.interval = TRUE, FDR.thrld = 0.05,
  PI.thrld = c(0.4, 0.6), xlab = "gene rank",
  ylab = "probabilstic index", add.legend = TRUE, cols.seg = NULL,
  las = 1, cex.lab = 1.25, ylim = c(0, 1), col = NULL, pch = 20,
  cex = 0.5, lty.PI = 3, lwd.PI = 1.25, col.PI = "blue",
  legend.pos = "bottomright", pt.cex.legend = 1.25, cex.legend = 1,
  ...)

Arguments

pim.res	outputs from PIMSeq() function
contrast	a vector of coefficients for the linear combination of the factors
add.PI.interval	a logical value to add error bar
FDR.thrld	FDR threshold, a numerical value between 0 and 1
PI.thrld	a vector of numerical values for the down and up regulated genes PI threshold
xlab	xlab parameter for plot()
ylab	ylab parameter for plot()
add.legend	a logical value to add a legend
cols.seg	a vector of colors for the error bars. Size must be equal to the number of genes
las	las parameter for plot()
cex.lab	cex.lab parameter for plot()
ylim	ylim parameter for plot()
col	col parameter for plot()
pch	pch parameter for plot()
cex	cex parameter for plot()
lty.PI	lty parameter for plot(), for PI horizontal line(s)
lwd.PI	lwd parameter for plot(), for PI horizontal line(s)
col.PI	col parameter for plot(), for PI horizontal line(s)
legend.pos	legend position
pt.cex.legend	pch size for legend
cex.legend	size of legend
...	other graphical parameters for plot()

Value

plot

Examples

# see examples in PIMSeq() function

CenterForStatistics-UGent/PIMseq documentation built on Jan. 15, 2024, 3:49 a.m.