inst/doc/plots_schematic.R

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

## ---- echo = FALSE,hide=TRUE, message=FALSE, warning=FALSE--------------------
library(ELMER)
library(DT)
library(dplyr)
library(BiocStyle)

## ----eval=TRUE, message=FALSE, warning = FALSE, results = "hide"--------------
# Load results from previous sections
mae <- get(load("mae.rda"))
pair <- read.csv("result/getPair.hypo.pairs.significant.csv")

## ----results='hide', eval=TRUE,fig.height=5,  fig.cap="The schematic plot shows probe colored in blue and the location of nearby 20 genes. The genes significantly linked to the probe  were shown in red.", message=FALSE, warning=FALSE----
schematic.plot(pair = pair, 
               data = mae,
               group.col = "definition",
               byProbe = pair$Probe[1],
               save = FALSE)

## ----results='hide', eval=TRUE, fig.width=6, fig.height=10, fig.cap="The schematic plot shows the gene colored in red and all blue colored probes, which are significantly linked to the  expression of this gene."----
schematic.plot(pair = pair, 
               data = mae,   
               group.col = "definition", 
               byGene = pair$GeneID[1],
               save = FALSE)