msbnetplot: Visualization of MSB neighbors of interested genes.

In NWPU-903PR/Funm6AViewer: Visualization of single base differential m6A methylation sites and functional DmM genes

Description

Visualization of MSB neighbors of interested genes.

Usage

msbnetplot(genesymbol,
           dmgene,
           descore,
           orgsymbol = org.Hs.egSYMBOL,
           datapath = NA,
           savepath = NA,
           savename = NA,
           plotsize = NA,
           labeloff = FALSE)

Arguments

genesymbol	A vector of the gene symbol of interested genes to visualize
dmgene	A vector of the gene symbol of DmM genes
descore	A vector of named numbers denote the differntial expression score of all genes, it can be genarated using getdescore function
orgsymbol	The gene name annotation. You need to input it similar to "org.Hs.egSYMBOL" if DefaultGenome is use other genomes instead of human genome.
datapath	The file path where the network information required of FunDMDeepm6A, usually do not need to input, only if you prefer to use your own PPI networks
savepath	The file path where to save the result
savename	The name of the saved figure
plotsize	The size of the saved figure, by defalt, it is 6 when the number of MSB neighbors is no more than 50.
labeloff	Logical parameter that determine whether to display the gene name of MSB neighbors.

Details

msbnetplot is used to Visualize of MSB neighbors of one or more interested genes.

Value

By default, msbnetplot will output result of network of one or more FDmMGenes' MSB neighbors.

Author(s)

Songyao Zhang

References

Funm6AViewer: Visualization of single base differential m6A methylation sites and functional DmM genes.

Examples

## MSB net plot for interested gene

dminfo <- system.file("extdata", "DMinfo_toy.xls", package="Funm6AViewer")
deinfo <- system.file("extdata", "DEinfo_toy.xls", package="Funm6AViewer")

dminfo <- read.table(dminfo, header = TRUE, stringsAsFactors = FALSE)
deinfo <- read.delim(deinfo, header = TRUE, stringsAsFactors = FALSE)

dmgene <- unique(dminfo$name)
descore <- getdescore(deinfo)

siggene <- c("CCNT1", "MYC", "BCL2")

# The datapath is the filepath where the required PPI data saved, they can be downloaded
# from https://pan.baidu.com/s/1qOGG57OgxmrTwSbbBEeQ2w&shfl=sharepset
datapath <- "E:/Funm6A_package/data"

# plot for one gene
re <- msbnetplot(genesymbol = siggene[1], dmgene = dmgene, descore = descore, datapath = datapath)

# plot for several genes
re <- msbnetplot(genesymbol = siggene, dmgene = dmgene, descore = descore, datapath = datapath,
                 savename = "InterestedGene")

NWPU-903PR/Funm6AViewer documentation built on April 25, 2021, 4:26 p.m.