R: PCA plot

dba.plotPCA {DiffBind}

R Documentation

PCA plot

Description

Principal Component Analysis plot

Usage

dba.plotPCA(DBA, attributes, minval, maxval,
           contrast, method=DBA$config$AnalysisMethod, 
           th=DBA$config$th, bUsePval=DBA$config$bUsePval, 
           report, score, bLog=TRUE, mask, sites, label, cor=FALSE,
           b3D=FALSE, vColors, dotSize, labelSize, labelCols, 
           components=1:3, ...)

Arguments

DBA

DBA object.

`attributes`	attribute or vector of attributes to use to color plotted points. Each unique combination of attribute values will be assigned a color. Chosen from: DBA_GROUP DBA_ID DBA_TISSUE DBA_FACTOR DBA_CONDITION DBA_TREATMENT DBA_REPLICATE DBA_CONSENSUS DBA_CALLER Note that DBA_GROUP is a special attribute which will result in samples from each group in a contrast being colored separately.
`minval`	Set all scores less than this to minval
`maxval`	Set all scores greater than this to maxval
`contrast`	number of contrast to use for PCA; if present, plots a PCA based on a differential binding affinity analysis (see `dba.analyze`). If mask is unspecified, only the samples in the contrast will be included. See `dba.show(DBA, bContrast=T)` to get contrast numbers. If missing, uses scores in the main binding matrix.
`method`	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 PCA, subject to maxVal. Used in conjunction with contrast.
`bUsePval`	if TRUE, uses p-value instead of FDR for thresholding. Used in conjunction with contrast.
`report`	report (obtained from `dba.report`) specifying the data to be used . If this is present, the method, th, and bUsePval parameters are ignored.
`score`	Score to use for count data. Only used when plotting the global binding matrix (no contrast specified). One of: DBA_SCORE_READS DBA_SCORE_READS_MINUS DBA_SCORE_READS_FOLD DBA_SCORE_RPKM DBA_SCORE_RPKM_FOLD DBA_SCORE_TMM_READS_FULL DBA_SCORE_TMM_READS_EFFECTIVE DBA_SCORE_TMM_MINUS_FULL DBA_SCORE_TMM_MINUS_EFFECTIVE
`bLog`	Logical indicating that log2 values should be used. Only applicable to read count scores (not peak scores).
`mask`	mask indicating a subset of peaksets to use when using global binding matrix scores. If a contrast is specified, these peaksets will be included, but only the significantly differentially bound sites (using th, bUsePval, and/or report) will be included. See `dba.mask`.
`sites`	logical vector indicating which sites to include in PCA. Only relevant when using global binding matrix (contrast is missing).
`label`	A metadata field to use as a label in 2D plots. The value for this field will be written directly onthe plot near the dot for each sample. Values can be any of those vlaid for the `attributes` parameter.
`cor`	a logical value indicating whether the calculation should use the correlation matrix or the covariance matrix. Passed into princomp.
`b3D`	logical indicating that three principal components should be plotted (requires package{rgl}). If FALSE, the first two principal components are plotted.
`vColors`	vector of custom colors; is absent, default colors will be used.
`dotSize`	size of dots to plot; is absent, a default will be calculated.
`labelSize`	Scaling factor for labels if present. Default is 0.8.
`labelCols`	Vector of colors to use for labels. Default is "black".
`components`	Number(s) of the components to plot. Can be a vector of two or three component numbers, or a single integer. If an integer, that component, in addition to the succeeding one (`b3D=FALSE`) or two (`b3D=TRUE`) will be plotted.
`...`	arguments passed to plot or plot3d (rgl).

Details

MODE: PCA plot using significantly differentially bound sites:

dba.plotPCA(DBA, attributes, minval, maxval, contrast, method, th, bUsePval, b3D=F, vColors, dotSize, ...)

MODE: PCA plot using global binding matrix:

dba.plotPCA(DBA, attributes, minval, maxval, mask, sites, b3D=F, vColors, dotSize, ...)

Value

trellis plot from lattice package; see xyplot

Note

uses rgl package for 3D plots (if available)

Author(s)

Rory Stark

Examples

data(tamoxifen_peaks)

# peakcaller scores PCA
dba.plotPCA(tamoxifen)

# raw count correlation PCA
data(tamoxifen_analysis)
dba.plotPCA(tamoxifen)

#PCA based on normalized data for all sites
dba.plotPCA(tamoxifen,contrast=1,th=1)

#PCA based on DB sites only
p <- dba.plotPCA(tamoxifen,contrast=1)
p <- dba.plotPCA(tamoxifen,contrast=1,attributes=DBA_TISSUE)
p <- dba.plotPCA(tamoxifen,contrast=1,attributes=DBA_TISSUE,label=DBA_CONDITION)
p <- dba.plotPCA(tamoxifen,contrast=1,attributes=DBA_CONDITION,label=DBA_TISSUE)
p <- dba.plotPCA(tamoxifen,contrast=1,attributes=c(DBA_TISSUE,DBA_CONDITION),
                label=DBA_REPLICATE)

[Package DiffBind version 2.10.0 Index]