plotFeatureHeatmap: generates heatmap plot of feature statistics

Description Usage Arguments Details Author(s) See Also Examples

View source: R/plotFeatureHeatmap.R

Description

This function generates a heatmap plot of feature statistics across alpha, which includes statistical significance annotations for individual features. By default, features are selected (and ordered top-down) by statistical significance based on a given value of alpha; options are provided to customize feature selection and display.

Usage

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plotFeatureHeatmap(x, alpha.index=NULL, stat=c("freq","coef"), feature.all, feature.pval.thres, 
feature.set, feature.top.n, signif.code, xlab=NULL, ylab=NULL, main=NULL, 
col.main="black", cex.main=0.95, line=1, col=NULL, breaks=NULL, scale="none", 
Rowv=F, Colv=F, na.color=NULL, cexRow=NULL, srtRow=0, cexCol=0.75, srtCol=45, 
margins=c(5, 5), key=T, key.title=NA, dendogram="none", trace="none", 
notecol.freq="black", notecol.coef="white", notecex=1, subtitle1=NULL, 
col.subtitle1="black", line.subtitle1=-1, cex.subtitle1=0.65, subtitle2=NULL, 
col.subtitle2="darkgray", line.subtitle2=-2, cex.subtitle2=0.55, ...)

Arguments

x

eNetXplorer object.

alpha.index

Integer indices to select alpha values. Default is 1:length(alpha)

stat

Feature statistic: "freq" for nonzero frequency, "coef" for mean nonzero coefficient.

feature.all

(Feature selection argument 1) Logical to show all features. Default is FALSE.

feature.pval.thres

(Feature selection argument 2) P-value threshold to select features. Default is NULL.

feature.set

(Feature selection argument 3) Character vector of feature names to display. Default is NULL.

feature.top.n

(Feature selection argument 4) Number of top features (ordered by p-value) to display. Default is 25.

signif.code

Logical to display statistical significance annotations. Default is TRUE.

xlab

Label for x axis.

ylab

Label for y axis.

main

Custom title.

col.main

Title color.

cex.main

Title size.

line

Title location.

col

Heatmap color vector. Length must be one less than number of breaks.

breaks

Color breaks vector. Default number of breaks is 10.

scale

Logical to scale the data for heatmap in either the row or column direction. Default is "none".

Rowv

Logical to reorder rows by hierarchical clustering. Default is FALSE.

Colv

Logical to reorder columns by hierarchical clustering. Default is FALSE.

na.color

Color to use for missing values.

cexRow

Size of row labels.

srtRow

Angle of row labels, in degrees from horizontal.

cexCol

Size of column labels.

srtCol

Angle of column labels, in degrees from horizontal.

margins

Numeric vector of length 2 containing the margins for column and row names, respectively.

key

Logical to display key. Default is TRUE.

key.title

Main title of the color key.

dendogram

To draw dendograms. Default is "none".

trace

To display trace lines. Default is "none".

notecol.freq

Color of statistical significance annotations for feature frequency heatmaps.

notecol.coef

Color of statistical significance annotations for feature coefficient heatmaps.

notecex

Size of significance annotations.

subtitle1

Custom subtitle 1.

col.subtitle1

Color of subtitle 1.

line.subtitle1

Position of subtitle 1.

cex.subtitle1

Size of subtitle 1.

subtitle2

Custom subtitle 2.

col.subtitle2

Color of subtitle 2.

line.subtitle2

Position of subtitle 2.

cex.subtitle2

Size of subtitle 2.

...

Additional plotting parameters.

Details

Feature selection criteria are hierarchical based on arguments 1 through 4 (see argument description above), with argument 1 at the top of the hierarchy. E.g. if feature.all is explicitly set to TRUE, it will take precedence over any other feature selection argument. By default, the top 25 features are displayed, ordered top-down by significance based on the given value of alpha.

Author(s)

Julian Candia and John S. Tsang
Maintainer: Julian Candia [email protected]

See Also

eNetXplorer, plot

Examples

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## Not run: 
data(QuickStartEx)
fit = eNetXplorer(x=QuickStartEx$predictor,y=QuickStartEx$response,
family="gaussian",n_run=20,n_perm_null=10,seed=111)
plot(x=fit,plot.type="featureHeatmap",stat="freq")
plotFeatureHeatmap(x=fit,alpha.index=3,stat="freq",main="custom title")

## End(Not run)

juliancandia/eNetXplorer documentation built on April 22, 2018, 9:20 p.m.