TravisPlot: Plot the Transcriptomic View of Genomic Features with Travis...

In lzcyzm/Travis: Transcriptomic View of Genomic Features

Usage

TravisPlot(peak, TravisCoordsFromTxDb = NA, txdb = NA, genome = NA, saveToPDFprefix = NA)

Arguments

peak
TravisCoordsFromTxDb
txdb
genome
saveToPDFprefix

Note

Please let me know if you have any questions.

Author(s)

Jia Meng < [e-mail] >

Examples

# Find the toy data files came with Travis package
bed3=system.file("extdata", "H3K4me3_mm10_1000peaks.bed", package="Travis")
bed12=system.file("extdata", "m6A_mm10_exomePeak_1000peaks_bed12.bed", package="Travis")
bam1=system.file("extdata", "SRR568477_mm10_XIST.bam", package="Travis")
bam2=system.file("extdata", "SRR1768320_mm10_XIST.bam", package="Travis")

# Read 4 different kinds of Genomic Features into R
H3K4me3 <- import.bed(bed3) # bed3 imported as GRanges
m6A <- BED12toGRangesList(bed12) # bed12 imported as GRangesList
SRR568477 <- readGAlignments(bam1) # bam imported as GAlignments
SRR1768320 <- readGAlignments(bam2) # bam imported as GAlignments

# put everything in a list with names
peak <- list(H3K4me3,m6A,SRR568477,SRR1768320) 
names(peak) <- c("H3K4me3", "m6A", "BAM1", "BAM2")

# make TravisPlot
# show the transcriptomic view of 4 sets of genomic features

# OPTION 1
TravisPlot(peak, 
           genome="mm10", 
           saveToPDFprefix = "Toy")
# gene annotation will be downloaded automatically, 
# and two PDF figures with prefix "Toy" will be saved
# in the current working directory

# OPTION 2
# It takes a few minutes to built TravisCoodinatesFromTxDb,
# so we may want to reuse it to save some time.
txdb <- makeTxDbFromUCSC(genome="mm10")
TravisCoordsFromTxDb <- makeTravisCoordsFromTxDb(txdb)
TravisPlot(peak[1:2], 
           TravisCoordsFromTxDb = TravisCoordsFromTxDb, 
           saveToPDFprefix = "Toy2")
TravisPlot(peak[3:4], 
           TravisCoordsFromTxDb = TravisCoordsFromTxDb, 
           saveToPDFprefix = "Toy3")

# OPTION 3
# The function may return the figures which you may resize
tp <- TravisPlot(peak, TravisCoordsFromTxDb = TravisCoordsFromTxDb)
tp[[1]] # Please ignore the warning message
tp[[2]] # Please ignore the warning message
tp[[1]] + ylim(-1,5) # reset the range of y axis
tp[[2]] + ylim(-1,5) # reset the range of y axis

lzcyzm/Travis documentation built on May 21, 2019, 9:16 a.m.