4.2 - Schematic plots

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

library(ELMER)
library(DT)
library(dplyr)
library(BiocStyle)

Loading required data for plot

# Load results from previous sections
mae <- get(load("mae.rda"))
pair <- read.csv("result/getPair.hypo.pairs.significant.csv")

Schematic plot

Schematic plot shows a brief view of linkages between genes and probes.

Nearby Genes

Generate schematic plot for one probe with 20 nearby genes and label the gene significantly linked with the probe in red.

schematic.plot(pair = pair, 
               data = mae,
               group.col = "definition",
               byProbe = pair$Probe[1],
               save = FALSE)

Nearby Probes

Generate schematic plot for one gene with the probes which the gene is significantly linked to.

schematic.plot(pair = pair, 
               data = mae,   
               group.col = "definition", 
               byGene = pair$GeneID[1],
               save = FALSE)

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