DEP_Mod_HeatMap | R Documentation |
get the DEP enrich fold in Module and plot a HeatMap
DEP_Mod_HeatMap(DEP_Mod, xlab = "DEP", filter = c("p","p.adj"), cutoff = 0.05, filename = NULL, ...)
DEP_Mod |
a list of DEP_Mod enrichment information. data.frame in list is get from |
xlab |
it indicate x value in heatmap. it must be a value between " |
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. |
a list of enrich fold heatmap information.
enrichFold |
enrichFold of DEP in Modules. |
textMatrix |
siginificant enrichment module information. |
Kefu Liu
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)
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