groupPlot.family {ShotgunFunctionalizeR}R Documentation

Plots the result from a gene-centric direct comparison using the Poisson model

Description

groupPlot plots the result from a gene-centric direct comparison of two groups. The normalized rate is shown for each sample and the combined rate within each group is shown as a horizontal line. This function requires that the Poisson model has been fitted to the data.

Usage

groupPlot.family(stat.families, family, ylim, 
                 col=c("mistyrose", "lavender", "red3", "royalblue3"), 
                 xlab="", main, print.pvalue=FALSE, 
                 print.pvalue.pos="topright", print.pvalue.cex=1.3)

Arguments

stat.families results from a direct comparison using the Poisson model (testGeneFamilies.dircomp)
family character string indicating which gene family to plot
ylim y limit of the plot. A suitable value is calculated if omitted
col character vector with four element indicating the colors of the bars of the first group, the bars of the second group, the horizontal line of the first group and the horizontal line of the second group
xlab label of the x-axis
main the title of the plot. If omitted, the annotation of the gene family will be used
print.pvalue should the corresponding p-value be printed?
print.pvalue.pos where should be p-value be placed? This argument is analogous to the location keywords used by legend.
print.pvalue.cex the magnification of the text used to print the p-value

See Also

groupPlot, groupPlot.category, trendPlot,trendPlot.family,trendPlot.category

Examples

## Not run: 
data(MouseCOG)
po.stat<-testGeneFamilies.dircomp(MouseCOG, groups=c("Lean", "Lean", "Lean", "Obese", "Obese"))
groupPlot.family(po.stat, family="COG1662")
## End(Not run)

[Package ShotgunFunctionalizeR version 1.0-3 Index]