ELMER (version 1.4.2)

scatter.plot: scatter.plot to plot scatter plots between gene expression and DNA methylation.

Description

scatter.plot is a function to plot various scatter plots between gene expression and DNA methylation. When byPair is specified, scatter plot for individual probe-gene pairs will be generated. When byProbe is specified, scatter plots for one probes with nearby 20 gene pairs will be generated. When byTF is specified, scatter plot for TF expression and average DNA methylation at certain motif sites will be generated.

Usage

scatter.plot(mee, byPair = list(probe = c(), gene = c()), byProbe = list(probe = c(), geneNum = 20), byTF = list(TF = c(), probe = c()), category = NULL, dir.out = "./", save = TRUE, ...)

Arguments

mee

A MEE.data object includes DNA methylation data, expression data, probeInfo and geneInfo.

byPair

A list: byPair =list(probe=c(),gene=c()); probe contains a vector of probes' name and gene contains a vector of gene IDs. The length of probe should be the same with length of gene.

byProbe

A list byProbe =list(probe=c(), geneNum=20); probe contains a vector of probes' name and geneNum specify the number of gene near the probes will ploted. 20 is default for geneNum.

byTF

A list byTF =list(TF=c(), probe=c()); TF contains a vector of TF's symbol and probe contains the a vector of probes' name.

category

A vector labels subtype of samples or a character which is the column name in the sampleInfo in the MEE.data object. Once specified, samples will label different color. The color can be customized by using color.value.

dir.out

A path specifies the directory to which the figures will be saved. Current directory is default.

save

A logic. If true, figure will be saved to dir.out.

...

color.value, lm_line in scatter function

Value

Scatter plots.

Examples

load(system.file("extdata","mee.example.rda",package = "ELMER"))
scatter.plot(mee,byProbe=list(probe=c("cg19403323"),geneNum=20),
           category="TN", save=FALSE)
scatter.plot(mee,byProbe=list(probe=c("cg19403323"),geneNum=20),
           category="TN", save=TRUE) ## save to pdf
# b. generate one probe-gene pair
scatter.plot(mee,byPair=list(probe=c("cg19403323"),gene=c("ID255928")),
            category="TN", save=FALSE,lm_line=TRUE)