plotMdGsa: Plot Multi-Dimensional Gene Set

In mdgsa: Multi Dimensional Gene Set Analysis.

Description

Plots confidence region for a Gene Set in a two dimensional space.

Usage

plotMdGsa(index, block, cr = 0.95, pch = ".", pch.block = 20, lwd = 2,
  col.all = "blue", col.block = "red", project = FALSE,
  col.proj = "green", diagonals = FALSE, col.diag = "gray", ...)

Arguments

index	matrix or data frame with the two columns of ranking statistics.
block	matrix or data frame with gene ids in the first column and gene set ids in the second column.
cr	level of the confidence region.
pch	plotting character for all genes.
pch.block	plotting character for the genes in the gene set or functional block.
lwd	line width. Used when drawing ellipses and other lines.
col.all	color used to represent all genes.
col.block	color used to represent the genes in the gene set being plotted.
project	if TRUE projection over the axis are displayed for the genes of the gene set.
col.proj	color used to plot the projection.
diagonals	if TRUE diagonals are plotted.
col.diag	color used to plot the diagonals.
...	arguments to be passed to plot

Details

Black dots show all genes in the dataset. Red stars show the genes in the Gene Set. Blue axis show the "center" of the distribution of all genes; blue ellipse shows the confidence region for all genes. Red axis show the "center" of the distribution of the genes in the Gene Set; red ellipse shows the confidence region for genes in the Gene Set.

Value

A plot.

Author(s)

David Montaner [e-mail]

See Also

mdGsa, mdPat, mdPat, ellipsoidPoints

Examples

## Not run: 
res <- mdGsa (rindexMat, annotList)
plotMdGsa (rindexMat, block = annotList[["GO:0006915"]])

## End(Not run)

mdgsa documentation built on Nov. 8, 2020, 5:05 p.m.