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Last data update: 2014.03.03

R: Draw a binding site heatmap

dba.plotHeatmap

R Documentation

Draw a binding site heatmap

Description

Draws a binding site heatmap

Usage

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,
                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 present, 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 int he order they are appear int he lcusteruing plot), with the values being the actual plotted values.

Author(s)

Rory Stark

Examples

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> 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.plotHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dba.plotHeatmap
> ### Title: Draw a binding site heatmap
> ### Aliases: dba.plotHeatmap
> 
> ### ** Examples
> 
> 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
GRanges object with 1000 ranges and 11 metadata columns:
       seqnames               ranges strand |            BT4742
          <Rle>            <IRanges>  <Rle> |         <numeric>
  1394    chr18 [37893179, 37893679]      * |   5.6655328175932
   914    chr18 [24642724, 24643224]      * |  4.55005560017327
  1150    chr18 [31592697, 31593197]      * |  6.13501810089442
  1368    chr18 [37115976, 37116476]      * |  4.90369255478797
  1272    chr18 [34100800, 34101300]      * |  6.40249841175941
   ...      ...                  ...    ... .               ...
   707    chr18 [20424038, 20424538]      * | 0.380130598730957
  1903    chr18 [51217759, 51218259]      * | 0.380130598730957
  1228    chr18 [33102434, 33102934]      * | 0.380130598730957
  2390    chr18 [62103300, 62103800]      * | 0.380130598730957
  1966    chr18 [52596076, 52596576]      * | 0.380130598730957
                  BT4741           MCF7r1           MCF7r2            MCF71
               <numeric>        <numeric>        <numeric>        <numeric>
  1394  4.85121369798651 1.70652043730863 2.74486545709392 1.00169390113662
   914  5.41309258559462 3.29148293802979 2.15990295637277 1.00169390113662
  1150  6.15933599334884 2.29148293802979 1.15990295637277 1.00169390113662
  1368  4.85121369798651 0.70652043730863 3.15990295637277 2.58665640185778
  1272  6.21378377737121 0.70652043730863 3.15990295637277 1.00169390113662
   ...               ...              ...              ...              ...
   707 0.458896275207745 0.70652043730863 2.15990295637277 1.00169390113662
  1903 0.458896275207745 0.70652043730863 2.15990295637277 1.00169390113662
  1228 0.458896275207745 0.70652043730863 1.15990295637277 1.00169390113662
  2390 0.458896275207745 0.70652043730863 1.15990295637277 1.00169390113662
  1966 0.458896275207745 0.70652043730863 1.15990295637277 1.00169390113662
                   MCF73            MCF72             ZR751            ZR752
               <numeric>        <numeric>         <numeric>        <numeric>
  1394 0.550628427645601  3.2040744803403 0.464373801530046 2.40877635240219
   914   1.5506284276456 3.52600257522766  1.20133939569625 2.26675734752976
  1150  2.13559092836676 2.78903698106145   2.0493363022512 2.76632835702027
  1368   2.5506284276456  1.2040744803403                 0 1.10921607054328
  1272   1.5506284276456 2.78903698106145  0.87941130080889                0
   ...               ...              ...               ...              ...
   707 0.550628427645601  1.2040744803403  3.68676622286649 3.69417857126444
  1903 0.550628427645601  1.2040744803403  4.30567605551099 4.26675734752976
  1228 0.550628427645601  1.2040744803403   3.0493363022512 3.47486554285996
  2390 0.550628427645601  1.2040744803403  2.68676622286649 2.83504110710429
  1966 0.550628427645601  1.2040744803403  2.78630189641741 3.05263254217691
                  T47D2            T47D1
              <numeric>        <numeric>
  1394  2.8869596780919 2.61850034530758
   914 3.37238650526214 1.61850034530758
  1150 3.73495658464685 1.61850034530758
  1368 3.47192217881305 1.61850034530758
  1272  2.8869596780919 4.78842534674989
   ...              ...              ...
   707 4.51922789359141 4.42585526736518
  1903 4.60942570256299  5.5253909409161
  1228 4.20888777297926 4.42585526736518
  2390 3.73495658464685 3.94042844019494
  1966  3.9573490059833 4.20346284602874
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> 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)
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
> # 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)  
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>