DEP_Mod_net_plot {DDPNA}

DEP_Mod_net_plot

Description

remove hubs which is not in the IDsets and replot the PFG network

Usage

DEP_Mod_net_plot(ModNet, IDsets = NULL, data = NULL, module = NULL,
                 plot = TRUE, filename = NULL, filetype = "pdf",
                 OnlyPlotLast = TRUE, BranchCut = TRUE,
                 reconstructNet = TRUE,
                 iteration = Inf, label.hubs.only = TRUE,
                 node.default.color = "grey",
                 hubLabel.col = "black", ...)

Arguments

ModNet

data contains network information which get from getmoduleHub

IDsets

ID sets information which get from DEPsets

data

the value should be defined only when reconstructNet is TRUE. The value is proteomic quantification data, which is same as the input in getmoduleHub.

module

the value should be defined only when reconstructNet is TRUE. The value is module information which is same as the input in getmoduleHub.

plot

a logical value whether plot a picture.

filename

the filename of plot. The default value is NULL which means no file saving. The function is use ggsave to achieve.

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).

OnlyPlotLast

a logical value whether plot the final network.

BranchCut

a logical value whether remove unhub proteins which have no connection to DEPs.

reconstructNet

a logical value whether reconstruct network.

iteration

iteration times when reconstruct network.

label.hubs.only

a logical value whether show labels for hubs only.

node.default.color

Default node colors for those that do not intersect with signatures in gene.set.

hubLabel.col

Label color for hubs.

...

additional ggsave parameter

Value

a list contains network information

netgene

all IDs in network.

hub

hub IDs

PMFG

PMFG graph data frame information

Author(s)

Kefu Liu

Examples

data(net)
data(imputedData)
Module <- Module_inf(net, imputedData$inf)
group <- gsub("[0-9]+","", colnames(imputedData$intensity))
data <- imputedData
data$inf <- data$inf[1:100,]
data$intensity <- data$intensity[1:100,]
stat <- dataStatInf(data, group, meanmethod = "median",
                    T.test = "pairwise", Aadj = "fdr",
                    Tadj = "fdr", cutoff = FALSE)
stat1 <- stat$ori.ID[stat$ad > 1]
stat2 <- stat$ori.ID[stat$asym > 1]
datalist <- list(stat1 = stat1, stat2 = stat2)
sets <- DEPsets(datalist)

logD <- imputedData$log2_value
rownames(logD) <- imputedData$inf$ori.ID
Mod3 <- getmoduleHub(logD, Module, 3, coln = "ori.ID", adjustp = FALSE)

newnet <- DEP_Mod_net_plot(Mod3, sets,
                           data = logD, module = Module,
                           plot = FALSE, filename = NULL, filetype = "pdf",
                           OnlyPlotLast = FALSE,reconstructNet = FALSE)