camerplot: cameraplot
In mskilab/skitools: Various mskilab R utilties

camerplot

R Documentation

cameraplot

Description

plots the results of CAMERA in limma package

Usage

cameraplot(
  camera.res,
  gene.sets,
  voom.res = NULL,
  design = NULL,
  genes = NULL,
  contrast = ncol(design),
  title = "Camera Gene set notch plot",
  cex.space = 1,
  col.axis = alpha("gray20", 0.8),
  col.ramp = c("blue", "red"),
  cex.slab = 1,
  cex.glab = 1,
  lwd.notch = 1,
  tick.w = 0.1,
  max.genes = 10,
  text.shift = 0.5,
  height.wf = 0.1,
  min.corr = 0.1,
  min.dist = 10,
  middle = NULL,
  max.gene.sets = 20,
  gtext.shift = 0.2
)

Arguments

`camera.res`	output of camera from limma, or data.table with fields $name, $P, $Direction, $FDR
`gene.sets`	gene set input to camera (named list of indices into the voom.res gene expression matrix)
`voom.res`	output of voom from limma (default NULL)
`design`	design matrix input to camera (default NULL)
`genes`	alternate to voom.res and design can just provide a named numeric vector of effect sizes, named by genes
`cex.space`	label spacing expansion factor (use if labels get too crowded
`col.axis`	axis color character
`col.ramp`	ramp from lowest to highest expression to phenotype correlation (default blue, red)
`cex.slab`	set label cex
`cex.glab`	gene label cex
`lwd.notch`	notch thickness
`max.genes`	max genes to draw in "leading edge" of gene set
`text.shift`	minimal distance between labels
`height.wf`	height of the topmost correlation waterfall plot
`min.corr`	minimal abs(correlation) value for leading edge definition