dba.plotHeatmap: Draw a binding site heatmap

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/DBA.R

Description

Draws a binding site heatmap

Usage

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dba.plotHeatmap(DBA, attributes=DBA$attributes, maxSites=1000, minval, maxval,
                contrast, method=DBA$config$AnalysisMethod, 
                th=DBA$config$th, bUsePval=DBA$config$bUsePval, 
                report, score, bLog=TRUE, mask, sites, sortFun=sd,
                correlations=TRUE, olPlot=DBA_COR, 
                ColAttributes,RowAttributes, colSideCols, rowSideCols=colSideCols,
                margin=10, colScheme="Greens", distMethod="pearson",
                ...)

Arguments

DBA

DBA object.

attributes

attribute or vector of attributes to use for column labels:

  • DBA_ID

  • DBA_TISSUE

  • DBA_FACTOR

  • DBA_CONDITION

  • DBA_TREATMENT

  • DBA_REPLICATE

  • DBA_CONSENSUS

  • DBA_CALLER

maxSites

maximum number of binding sites to use in heatmap. Only used when not drawing a correlation heatmap (correlations=FALSE)

minval

Set all scores less than this to minval

maxval

Set all scores greater than this to maxval

contrast

number of contrast to report on; if present, draws a heatmap based on a differential binding affinity analysis (see dba.analyze). Only significantly differentially bound sites will be used (subject to the th and bUsePval parameters). 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

analysis method (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 report (subject to maxSites). Used in conjunction with contrast.

bUsePval

logical indicating whether to use FDR (FALSE) or p-value (TRUE) 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. Used in conjunction with contrast.

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.

sites

logical vector indicating which sites to include; first maxSites of these. Only relevant when using global binding matrix (contrast is missing).

sortFun

function taking a vector of scores and returning a single value. Only relevant when using global binding matrix (contrast is missing). If not equal to FALSE, the global binding matrix will be sorted (descending) on the results, and the first maxSites used in the heatmap. Recommended sort function options include sd, mean, median, min.

correlations

logical indicating that a correlation heatmap should be plotted (TRUE). If FALSE, a binding heatmap of scores/reads is plotted. This parameter can also be set to a correlation record; see dba.overlap(mode=DBA_OLAP_ALL), in which case a correlation heatmap is plotted based on the specified correlation record, using the statistic specified in olPlot.

olPlot

if correlations is specified as a dataframe returned by dba.overlap, indicates which statistic to plot. One of:

  • DBA_COR Correlation

  • DBA_OLAP Percentage overlap

  • DBA_INALL number of peaks common to both samples

ColAttributes

Attribute or vector of attributes to plot for column color bars. If missing, all attributes with two or more unique non-NA values will be plotted. (For correlation heatmaps, DBA_GROUP will be plotted in the column color bar by default when a contrast is specified). A value of NULL indicates that no column color bar should be drawn. Allowable attribute values include:

  • DBA_GROUP

  • DBA_TISSUE

  • DBA_FACTOR

  • DBA_CONDITION

  • DBA_TREATMENT

  • DBA_REPLICATE

  • DBA_CALLER

RowAttributes

Attribute or vector of attributes for row color bars. Row color bars are only allowed for correlation heatmaps. Same values as for ColAttributes parameter. Default is to draw a row color bar only if a contrast is specified, in which case the plotted attribute is DBA_GROUP.

rowSideCols

Vector of colors to use in row color bars. Uses default colors if missing. Can also be a list of color vectors.

colSideCols

Vector of colors to use in column color bars. Uses default colors if missing. Can also be a list of color vectors.

margin

margin size of plot

colScheme

Color scheme; see colorRampPalette RColorBrewer

distMethod

distance method for clustering; see Dist

...

passed on to heatmap.2 (gplots), e.g. scale etc.

Details

MODE: Correlation Heatmap plot using statistics for global binding matrix:

dba.plotHeatmap(DBA, attributes=DBA$attributes, minval, maxval, correlations, olPlot, colScheme="Greens", distMethod="pearson", ...)

MODE: Correlation Heatmap plot using statistics for significantly differentially bound sites:

dba.plotHeatmap(DBA, attributes=DBA$attributes, minval, maxval, contrast, method=DBA_DESEQ2, th=0.05, bUsePval=F, mask, overlaps, olPlot=DBA_COR, colScheme="Greens", distMethod="pearson", ...)

MODE: Binding heatmap plot using significantly differentially bound sites:

dba.plotHeatmap(DBA, attributes, maxSites, minval, maxval, contrast, method, th, bUsePval, correlations=FALSE, colScheme, distMethod, ...)

MODE: Binding heatmap plot using the global binding matrix:

dba.plotHeatmap(DBA, attributes, maxSites, minval, maxval, mask, sites, correlations=FALSE, sortFun, colScheme, distMethod, ...)

Value

if correlations is not FALSE, the overlap/correlation matrix is returned.

if correlations is FALSE, the sites used in the heatmap are returned in a GRanges object, in the row order they appear (top to bottom). The metadata contains a column for each sample (also in the order they are appear in the clustering plot), with the values being the actual plotted values.

Author(s)

Rory Stark

See Also

dba.overlap

Examples

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data(tamoxifen_peaks)
# peak overlap correlation heatmap
dba.plotHeatmap(tamoxifen)

data(tamoxifen_counts)
# counts correlation heatmap
dba.plotHeatmap(tamoxifen)

data(tamoxifen_analysis)
#correlation heatmap based on all normalized data
dba.plotHeatmap(tamoxifen,contrast=1,th=1)

#correlation heatmap based on DB sites only
dba.plotHeatmap(tamoxifen,contrast=1)

#binding heatmap based on DB sites
dba.plotHeatmap(tamoxifen,contrast=1,correlations=FALSE)

#binding heatmap based on 1,000 sites with highest variance
sites <- dba.plotHeatmap(tamoxifen,contrast=1,th=1,
                         correlations=FALSE,sortFun=var)
sites

data(tamoxifen_counts)
#Examples of  heatmaps using DB sites with different subsets of samples
#exclude T47D
tamoxifen <- dba.contrast(tamoxifen,tamoxifen$masks$Resistant,c(3:5,10:11)) 
tamoxifen <- dba.analyze(tamoxifen,bCorPlot=FALSE)
# regular heatmaps with two contrast groups
dba.plotHeatmap(tamoxifen, contrast=1) 
#also include the T47D samples
dba.plotHeatmap(tamoxifen,contrast=1,mask=tamoxifen$masks$All) 
#correlation heatmap without MCF7 
plot(tamoxifen,contrast=1,mask=!tamoxifen$masks$MCF7) 
# binding heatmap using only the MCF7 samples
dba.plotHeatmap(tamoxifen,contrast=1,mask=tamoxifen$masks$MCF7,correlations=FALSE)  

DiffBind documentation built on Nov. 1, 2018, 2:38 a.m.