Getting Started with Travis Package
Intall Travis package and its dependencies
Install exomePeak, this will install a few useful packages from Bioconductor
source("http://bioconductor.org/biocLite.R")
biocLite("exomePeak")Install ggplot2, devtools and then Travis package
install.packages("ggplot2")
install.packages("devtools")
library(devtools)
install_github('lzcyzm/Travis')load Travis package
library(Travis)## Loading required package: Rsamtools
## Loading required package: S4Vectors
## Loading required package: stats4
## Loading required package: BiocGenerics
## Loading required package: parallel
##
## Attaching package: 'BiocGenerics'
##
## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB
##
## The following object is masked from 'package:stats':
##
## xtabs
##
## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, as.vector, cbind,
## colnames, do.call, duplicated, eval, evalq, Filter, Find, get,
## grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rep.int, rownames, sapply,
## setdiff, sort, table, tapply, union, unique, unlist, unsplit
##
## Loading required package: IRanges
## Loading required package: GenomeInfoDb
## Loading required package: GenomicRanges
## Loading required package: XVector
## Loading required package: Biostrings
## Loading required package: GenomicFeatures
## Loading required package: AnnotationDbi
## Loading required package: Biobase
## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
##
## Loading required package: rtracklayer
## Loading required package: GenomicAlignments
## Loading required package: SummarizedExperiment
## Loading required package: ggplot2Read all the toy data files into a list with names
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## [1] "Converting BED12 to GRangesList"
## [1] "It may take a few minutes"SRR568477 <- readGAlignments(bam1) # bam imported as GAlignments
SRR1768320 <- readGAlignments(bam2) # bam imported as GAlignmentsPut everything in a list with names
peak <- list(H3K4me3,m6A,SRR568477,SRR1768320)
names(peak) <- c("H3K4me3", "m6A", "BAM1", "BAM2")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 time.
txdb <- makeTxDbFromUCSC(genome="mm10") # Gene annotation downloaded from UCSC
TravisCoordsFromTxDb <- makeTravisCoordsFromTxDb(txdb) # TravisCoordinates generated
TravisPlot(peak[1:2],
TravisCoordsFromTxDb = TravisCoordsFromTxDb,
saveToPDFprefix = "Toy2")
TravisPlot(peak[3:4],
TravisCoordsFromTxDb = TravisCoordsFromTxDb,
saveToPDFprefix = "Toy3")two PDF figures with prefix “Toy2” and “Toy3” will be saved in the current working directory.
OPTION 3
Alternatively, the function may return the figures if saveToPDFprefix is not set.
tp <- TravisPlot(peak, genome="mm10")## [1] "Downloading Transcriptome Information from UCSC ..."
## [1] "Making Travis Coordinates ..."
## [1] "total 63244 transcripts extracted ..."
## [1] "total 49531 transcripts left after ambiguity filter ..."
## [1] "total 18997 mRNAs left after component length filter ..."
## [1] "total 7692 ncRNAs left after ncRNA length filter ..."
## [1] "Building Travis Coordinates. It may take a few minutes ..."
## [1] "Travis Coordinates Built ..."
## [1] "Figures returned as objects ..."
## [1] "Please check ..."tp[[1]] # Please ignore the warning message## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density
tp[[2]] # Please ignore the warning message## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density
you may resize the Y-axis of the two figures with the rules in ggplot2 package.
tp[[1]] + ylim(-1,5) # reset the range of y axis. Please ignore the warning message## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density
tp[[2]] + ylim(-1,5) # reset the range of y axis. Please ignore the warning message## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density## Warning in density.default(data$x, adjust = adjust, kernel = kernel, weight
## = data$weight, : sum(weights) != 1 -- will not get true density
Session Information
sessionInfo()## R version 3.2.1 (2015-06-18)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 8 x64 (build 9200)
##
## locale:
## [1] LC_COLLATE=English_United States.1252
## [2] LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] Travis_0.1.0 ggplot2_1.0.1
## [3] GenomicAlignments_1.5.9 SummarizedExperiment_0.2.3
## [5] rtracklayer_1.29.11 GenomicFeatures_1.21.13
## [7] AnnotationDbi_1.31.17 Biobase_2.29.1
## [9] Rsamtools_1.21.10 Biostrings_2.37.2
## [11] XVector_0.9.1 GenomicRanges_1.21.15
## [13] GenomeInfoDb_1.5.8 IRanges_2.3.12
## [15] S4Vectors_0.7.7 BiocGenerics_0.15.2
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.11.6 formatR_1.2 futile.logger_1.4.1
## [4] plyr_1.8.3 bitops_1.0-6 futile.options_1.0.0
## [7] tools_3.2.1 zlibbioc_1.15.0 biomaRt_2.25.1
## [10] digest_0.6.8 evaluate_0.7 RSQLite_1.0.0
## [13] gtable_0.1.2 DBI_0.3.1 proto_0.3-10
## [16] stringr_1.0.0 knitr_1.10.5 grid_3.2.1
## [19] XML_3.98-1.2 BiocParallel_1.3.27 rmarkdown_0.7
## [22] reshape2_1.4.1 lambda.r_1.1.7 magrittr_1.5
## [25] MASS_7.3-41 scales_0.2.5 htmltools_0.2.6
## [28] colorspace_1.2-6 labeling_0.3 stringi_0.5-5
## [31] munsell_0.4.2 RCurl_1.95-4.6