DEP_Mod_HeatMap {DDPNA}

DEP_Mod_HeatMap

Description

get the DEP enrich fold in Module and plot a HeatMap

Usage

DEP_Mod_HeatMap(DEP_Mod, xlab = "DEP", filter = c("p","p.adj"),
                cutoff = 0.05, filename = NULL, ...)

Arguments

DEP_Mod

a list of DEP_Mod enrichment information. data.frame in list is get from Module_Enrich function.

xlab

it indicate x value in heatmap. it must be a value between "DEP" and "MOD".

filter

p value or p.adjust value used to filter the enrich significant module.

cutoff

a numeric value is the cutoff of p value. Larger than the value will remove to show in plot.

filename

plot filename. If filename is null, it will print the plot.

...

other argument.

Value

a list of enrich fold heatmap information.

enrichFold

enrichFold of DEP in Modules.

textMatrix

siginificant enrichment module information.

Author(s)

Kefu Liu

Examples

data(net)
data(imputedData)
data <- imputedData
logD <- data$log2_value
rownames(logD) <- data$inf$ori.ID
group <- gsub("[0-9]+","", colnames(logD))
Module <- Module_inf(net, data$inf)
# define 2 DEP ID data: a and b
a <- Module$ori.ID[1:100]
b <- Module$ori.ID[50:100]
a <- Module_Enrich(Module, a, coln="ori.ID", enrichtype = "ORA")
b <- Module_Enrich(Module, b, coln="ori.ID", enrichtype = "ORA")
rowname <- a$module.name;
a <- data.frame(Counts = a$Counts, module.size = a$module.size,
                precent = a$precent, p = a$p, p.adj = a$p.adj,
                Z.score = a$Z.score, stringsAsFactors = FALSE)
rownames(a) <- rowname;
rowname <- b$module.name;
b <- data.frame(Counts = b$Counts, module.size = b$module.size,
                precent = b$precent, p = b$p, p.adj = b$p.adj,
                Z.score = b$Z.score, stringsAsFactors = FALSE)
rownames(b) <- rowname;
DEP_Mod <- list(a = a , b = b)
heatMapInf <- DEP_Mod_HeatMap(DEP_Mod)