RangedData table containing read positions,
i.e. output from get.reads. To ensure a useful ordering of the bars, the
chromosome information ('spaces' of reads) should be given as "chr" plus a
number/letter [plus further specification], e.g. "chr1", "chrX", "chr17_ctg5_hap1", "chrUn_gl000211".
targets
Optional RangedData table containing positions
of target regions, i.e. output from get.targets. The chromosome information should match
the one of reads. If targets is missing, only numbers of reads will be displayed.
plotchroms
character vector specifying the chromosomes that shall be included in the plot (and their desired order)
col
color(s) of the bars
ylab
y-axis label
legendpos
Position of the legend. String from the list "bottomright", "bottom", "bottomleft",
"left", "topleft", "top", "topright", "right" and "center". Ignored if targets is missing.
...
graphical parameters passed to barplot
Details
If targets is not specified, absolute read counts per chromosome are shown in the barplot.
If targets is provided, fractions of reads and targets are shown. For reads, this is the
fraction within the total number of reads (since reads are expected to have all the same length).
In contrast, for the targets, the fraction of targeted bases on each chromosome is calculated.
Since targets might vary in length it is reasonable to account for the actual target sizes instead
of considering merely numbers of targets per chromosome.
Value
Barplot of reads and optionally targets per chromosome.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'license()' or 'licence()' for distribution details.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(TEQC)
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 objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: hwriter
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TEQC/chrom.barplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chrom.barplot
> ### Title: Reads per chromosome barplot
> ### Aliases: chrom.barplot
> ### Keywords: hplot
>
> ### ** Examples
>
> ## get reads and targets
> exptPath <- system.file("extdata", package="TEQC")
> readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
> reads <- get.reads(readsfile, idcol=4, skip=0)
[1] "read 19546 sequenced reads"
> targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
> targets <- get.targets(targetsfile, skip=0)
[1] "read 50 (non-overlapping) target regions"
Warning message:
the "reduce" method for RangedData object is deprecated
>
> chrom.barplot(reads, targets)
>
>
>
>
>
> dev.off()
null device
1
>