An object of type list, giving a list of bam files. If you only have 1 file, use list(bam_file)
type
An object of type character. Can be qwidth,rname or strand. In theory, any column property existing in the bam file can be used, but these 3 would be most meaningful.
samplenames
Labels for the plot.
unique
Logical value to use unique reads (TRUE) or all reads (FALSE)
ncounts
Number of total counts in the bam file, used if unique is set to FALSE.
norm
Logical value to determine if plot will be normalised.
yname
y axis label.
Author(s)
Diana H.P. Low
Examples
data(ssviz)
plotDistro(list(ctrlbam))
Results
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(ssviz)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
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 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: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: reshape
Attaching package: 'reshape'
The following objects are masked from 'package:S4Vectors':
expand, rename
Loading required package: ggplot2
Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ssviz/plotDistro.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDistro
> ### Title: plotDistro
> ### Aliases: plotDistro
>
> ### ** Examples
>
> data(ssviz)
> plotDistro(list(ctrlbam))
No counts column provided in bam file. Running unique counts.
Otherwise provide a count matrix or run getCountMatrix.
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.