plotMdGsa {mdgsa} | R Documentation

## Plot Multi-Dimensional Gene Set

### 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 dmontaner@cipf.es

### See Also

`mdGsa`, `mdPat`, `mdPat`, `ellipsoidPoints`

### Examples

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

    ## End(Not run)

[Package mdgsa version 1.19.0 Index]