trendPlot.family {ShotgunFunctionalizeR}R Documentation

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

Description

trendPlot.family plots the result from a gene-centric regression analysis. The normalized rate is shown for each sample together with the fitted trend line. This function requires that the Poisson model has been fitted to the data.

Usage

trendPlot.family(stat.families, family, x.axis.lab=NULL, xlim, ylim,
                 col.points="black", col.text="grey30", col.trend="red3", 
                 xlab="", plot.counts=TRUE, main, 
                 print.pvalue=FALSE, print.pvalue.pos="topright", print.pvalue.cex=1.3, 
                 add=FALSE, ...)

Arguments

stat.families results from a regression analysis using the Poisson model (testGeneFamilies.regression)
family character string indicating which gene family to plot
x.axis.lab character vector with labels for the ticks at the x-axis
xlim x limit of the plot. A suitable value is calculated if omitted
ylim y limit of the plot. A suitable value is calculated if omitted
col the color on the 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
col.points color of the data points
col.text color of the text showing the number of counts
col.trend color of the fitted trend line
xlab label of the x-axis
plot.counts should the counts be plotted next to the data points?
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
add should a new plot be opened or should the figure be added to an existing plot?
... additional arguments for plot

See Also

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

Examples

## Not run: 
data(OceanCOG)
po.stat<-testGeneFamilies.regression(OceanCOG, covariates=c(10, 70, 130, 200, 500, 770, 4000), log.covariates=T)
trendPlot.family(po.stat, family="COG0415")
## End(Not run)

[Package ShotgunFunctionalizeR version 1.0-3 Index]