scatter.plot: scatter.plot to plot scatter plots between gene expression...

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

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(data, 
             byPair = list(probe = c(), gene = c()),
             byProbe = list(probe = c(), numFlankingGenes = 20), 
             byTF = list(TF = c(), probe = c()),
             category = NULL,
             ylim = NULL,
             dots.size = 0.9,
             correlation = FALSE,
             width = 7,
             height = 6,
             dir.out = "./",
             save = TRUE, ...)

Arguments

data	A multiAssayExperiment with DNA methylation and Gene Expression data. See createMAE function.
byPair	A list: byPair =list(probe=c(),gene=c()); probe contains a vector of probes' name and gene contains a vector of gene ID. The length of probe should be the same with length of gene. Output see numFlankingGenes
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 numFlankingGenes Output see detail.
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. Output see detail.
category	A vector labels subtype of samples or a character which is the column name in the colData(data) in the multiAssayExperiment object. Once specified, samples will label different color. The color can be customized by using color.value.
ylim	y-axis limit i.e. c(0,25)
dots.size	Control dots size
correlation	Add pearson correlation values to the plot
width	PDF width
height	PDF height
dir.out	A path specify 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

Details

byPair The output will be scatter plot for individual pairs.

byProbe The output will be scatter plot for the probe and nearby genes.

byTF The output will be scatter plot for the TFs and the average DNA methylation at the probes set specified in byTF list.

Value

Scatter plots.

Author(s)

Lijing Yao (maintainer: [e-mail])

Examples

data <- ELMER:::getdata("elmer.data.example")
scatter.plot(data,
            byProbe=list(probe=c("cg19403323"),numFlankingGenes=20), 
            category="definition", save=FALSE)
scatter.plot(data,byProbe=list(probe=c("cg19403323"),numFlankingGenes=20), 
            category="definition", save=TRUE) ## save to pdf
# b. generate one probe-gene pair
scatter.plot(data,byPair=list(probe=c("cg19403323"),gene=c("ENSG00000143322")),
             category="definition", save=FALSE,lm_line=TRUE) 

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.