allezPlot: Display an image of gene scores by functional sets

Description Usage Arguments Details Author(s) See Also Examples

Description

Plots functional sets against gene scores. Sets are ordered by highest sum of gene scores not in preceding sets, and genes are ordered by scores within set. Higher gene scores are indicated by darker color.

Usage

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allezPlot(allez.out, n.low = 5, n.upp = 500, n.cell=0, zthr = 3, gmax=20,
glab=c("none","gene_id","symbol"), slab=c("none","z.score","set.means"),
...)

Arguments

allez.out

list output from allez function, or concatenated output from allezC.

n.low

numeric, smallest number of genes in a set to consider for ranking

n.upp

numeric, largest number of genes in a set to consider for ranking

n.cell

numeric, minimum number of genes in a set with score>0, mainly used in conjunction with binary scores

zthr

numeric, keep sets with z-scores at this level or higher

gmax

numeric, maximum number of genes for x-axis labelling

glab

character string, adds gene labels to the x-axis: "none" indicates no gene labels, "gene_id" indicates entrez id, and "symbol" is gene symbol. Useful mainly for binary scores.

slab

character string, adds set statistics to right axis: "none" indicates no labels, "z.score" indicates z.score, and "set.means" is set means (from setscores element)

...

any extra arguments for text or axis, such as cex or cex.axis

Details

allezPlot creates an indicator matrix of the highest ranking sets using allezMat, adds gene score information, and orders the genes by highest ranking set and gene score.

If x-axis labelling is not chosen (glab = "none"), the plot width must be longer than the width of the set labels (the text appears in the plot region); the user may need to adjust the width of the figure in order to encompass the text.

If x-axis labelling is chosen (glab = "gene_id" or "symbol"), the plot width will be predefined, based on character size; the user may need to adjust the width of the figure in order to encompass the text.

Author(s)

Aimee Teo Broman and Michael Newton

See Also

allezMat allez

Examples

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data(npc)
scores  <- (1/2)*sqrt(28)*log((1-npc)/(1+npc))

npc.kegg <- allez( scores=scores, lib="hgu133plus2", sets="KEGG")

allezPlot(npc.kegg,zthr=5)

## Not run: 
npc.go <- allez( scores=scores, lib="hgu133plus2", sets="GO")
npc.all <- allezC(npc.go, npc.kegg)

allezPlot(npc.all,zthr=6)

## End(Not run)

atbroman/allez documentation built on May 10, 2019, 2:08 p.m.