groupPlot.family {ShotgunFunctionalizeR} | R Documentation |
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.
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)
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 |
groupPlot
, groupPlot.category
,
trendPlot
,trendPlot.family
,trendPlot.category
## 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)