method used for analysis (used in conjunction with contrast):
DBA_DESEQ2
DBA_DESEQ2_BLOCK
DBA_EDGER
DBA_EDGER_BLOCK
th
significance threshold; all sites with FDR (or p-values, see bUsePval) less than or equal to this value will be included in the boxplot.
bUsePval
logical indicating whether to use FDR (FALSE) or p-value (TRUE) for thresholding.
bNormalized
logical indicating that normalized data (using normalization factors computed by differential analysis method) should be plotted. FALSE uses raw count data.
attribute
attribute to use for determining groups of samples. Default (DBA_GROUP) plots the two groups used in the contrast. Possible values:
DBA_GROUP
DBA_ID
DBA_TISSUE
DBA_FACTOR
DBA_CONDITION
DBA_TREATMENT
DBA_REPLICATE
DBA_CONSENSUS
DBA_CALLER
bAll
logical indicating if plot should include a set of boxplots using all counts, regardless of whether or not they pass the significance threshold.
bAllIncreased
logical indicating if plot should include a set of boxplots using all counts that increase in affinity, regardless of whether or not they pass the significance threshold.
bAllDecreased
logical indicating if plot should include a set of boxplots using all counts that decrease in affinity, regardless of whether or not they pass the significance threshold.
bDB
logical indicating if plot should include a set of boxplots using all counts in significantly differentially bound sites (i.e. those that pass the significance threshold),
regardless of whether they increase or decrease in affinity.
bDBIncreased
logical indicating if plot should include a set of boxplots using all counts in significantly differentially bound sites that increase in affinity.
bDBDecreased
logical indicating if plot should include a set of boxplots using all counts in significantly differentially bound sites that decrease in affinity.
pvalMethod
method to use when computing matrix of p-values. If NULL, no matrix is computed, and NULL is returned; this may speed up processing if there are many boxplots.
bReversePos
logical indicating if the default definition of positive affinity (higher affinity in the second group of the contrast) should be reversed
(i.e. positive affinity is defined as being higher in the first group of the contrast).
attribOrder
vector of group numbers used to change the order that groups are plotted.
If NULL, default order is used (group order for DBA_GROUP, and the order the attribute values appear for other values of attribute).
vColors
vector of custom colors; if absent, default colors will be used.
varwidth
passed to boxplot
notch
passed to boxplot
...
other arguments passed to boxplot
Details
Draws a boxplot showing distributions of read counts for various groups of samples under various conditions.
In default mode, draws six boxes: one pair of boxes showing the distribution of read counts within all significantly differentially bound sites (one box for each sample group), one pair of boxes showing the distribution of read counts for significantly differentially bound sites that increase affinity in the second group,
and a second pair of boxes showing the distribution of read counts for significantly differentially bound sites that have higher mean affinity in the first group.
Value
if pvalMethod is not NULL, returns a matrix of p-values indicating the significance of the difference between each pair of distributions.
Author(s)
Rory Stark
Examples
data(tamoxifen_analysis)
#default boxplot includes all DB sites, then divided into those increasing
# affinity in each group
dba.plotBox(tamoxifen)
# plot non-normalized data for DB sites by tissue
# (changing order to place Resistant samples last)
dba.plotBox(tamoxifen, attribute=DBA_CONDITION, bDBIncreased=FALSE,
bDBDecreased=FALSE, attribOrder=c(2,1), bNormalized=FALSE)
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.
You are welcome to redistribute it under certain conditions.
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(DiffBind)
Loading required package: GenomicRanges
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
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DiffBind/dba.plotBox.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dba.plotBox
> ### Title: Boxplots
> ### Aliases: dba.plotBox
>
> ### ** Examples
>
> data(tamoxifen_analysis)
>
> #default boxplot includes all DB sites, then divided into those increasing
> # affinity in each group
> dba.plotBox(tamoxifen)
>
> # plot non-normalized data for DB sites by tissue
> # (changing order to place Resistant samples last)
> dba.plotBox(tamoxifen, attribute=DBA_CONDITION, bDBIncreased=FALSE,
+ bDBDecreased=FALSE, attribOrder=c(2,1), bNormalized=FALSE)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
