FCSenrichplot {DDPNA}R Documentation

FCSenrichplot

Description

plot of FCS enrichment analysis

Usage

FCSenrichplot(FCSenrich, count = 1, p = 0.05, filter = "p",
              plot = TRUE, filename = NULL,filetype = "pdf", ...)

Arguments

FCSenrich

FCS enrichment information which is getted in module_enrich function.

count

a numeric value. Module will choosed when countnumber is larger than count value .

p

a numeric value. Module will choosed when any Fisher's extract test p value is less than count value .

filter

filter methods. This must be (an abbreviation of) one of the strings "p","p.adj", "none".

plot

a logical value indicating whether draw enrichment variation trend plot.

filename

the filename of plot. The default value is NULL which means no file saving. The plot will be saved to "plot" folder.

filetype

the file type of plot. the type should be one of "eps", "ps", "tex" (pictex), "pdf", "jpeg", "tiff", "png", "bmp", "svg" or "wmf" (windows only).

...

Other arguments.

Author(s)

Kefu Liu

Examples

data(imputedData)
data(net)
data <- imputedData
logD <- data$log2_value
rownames(logD) <- data$inf$ori.ID
group <- gsub("[0-9]+","", colnames(logD))
Module <- Module_inf(net, data$inf)
pos<-which(Module$moduleNum %in% c(11:13))
up <- changedID(logD[pos,], group, vs.set2 = "ad",vs.set1 = "ctl",
              rank = "foldchange",anova = FALSE, Padj = "none",cutoff = 1,
              datatype = "log2",fctype = "up")
FCSenrich <- Module_Enrich(Module[pos,], up, coln="ori.ID")
FCSenrich <- FCSenrichplot(FCSenrich)


[Package DDPNA version 0.3.1 Index]