plotFeatureHeatmap | R Documentation |
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.
plotFeatureHeatmap(x, alpha.index=NULL, stat=c("freq","coef"), feature.all=FALSE,
feature.pval.thres=NULL, feature.set=NULL, feature.top.n=25, signif.code=TRUE,
xlab=NULL, ylab=NULL, main=NULL, col.main="black", cex.main=0.95, line=1,
col=NULL, breaks=NULL, scale="none", Rowv=FALSE, Colv=FALSE, na.color=NULL,
cexRow=NULL, srtRow=0, cexCol=0.75, srtCol=45, margins=c(5, 5), key=TRUE,
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, ...)
x |
|
alpha.index |
Integer indices to select |
stat |
Feature statistic: |
feature.all |
(Feature selection argument 1) Logical to show all features. Default is |
feature.pval.thres |
(Feature selection argument 2) P-value threshold to select features. Default is |
feature.set |
(Feature selection argument 3) Character vector of feature names to display. Default is |
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 |
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 |
Rowv |
Logical to reorder rows by hierarchical clustering. Default is |
Colv |
Logical to reorder columns by hierarchical clustering. Default is |
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 |
key.title |
Main title of the color key. |
dendogram |
To draw dendograms. Default is |
trace |
To display trace lines. Default is |
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. |
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
.
Julian Candia and John S. Tsang
Maintainer: Julian Candia julian.candia@nih.gov
eNetXplorer
, plot
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")
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