R 语言heatmap2 说明书.docx
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R 语言heatmap2 说明书.docx
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R语言heatmap2说明书
EnhancedHeatMap
Description
Aheatmapisafalsecolorimage(basically image(t(x)))withadendrogramaddedtotheleftsideand/ortothetop.Typically,reorderingoftherowsandcolumnsaccordingtosomesetofvalues(roworcolumnmeans)withintherestrictionsimposedbythedendrogramiscarriedout.
ThisheatmapprovidesanumberofextensionstothestandardR heatmap function.
Usage
heatmap.2(x,
#dendrogramcontrol
Rowv=TRUE,
Colv=if(symm)"Rowv"elseTRUE,
distfun=dist,
hclustfun=hclust,
dendrogram=c("both","row","column","none"),
symm=FALSE,
#datascaling
scale=c("none","row","column"),
na.rm=TRUE,
#imageplot
revC=identical(Colv,"Rowv"),
add.expr,
#mappingdatatocolors
breaks,
symbreaks=min(x<0,na.rm=TRUE)||scale!
="none",
#colors
col="heat.colors",
#blocksepration
colsep,
rowsep,
sepcolor="white",
sepwidth=c(0.05,0.05),
#celllabeling
cellnote,
notecex=1.0,
notecol="cyan",
na.color=par("bg"),
#leveltrace
trace=c("column","row","both","none"),
tracecol="cyan",
hline=median(breaks),
vline=median(breaks),
linecol=tracecol,
#Row/ColumnLabeling
margins=c(5,5),
ColSideColors,
RowSideColors,
cexRow=0.2+1/log10(nr),
cexCol=0.2+1/log10(nc),
labRow=NULL,
labCol=NULL,
#colorkey+densityinfo
key=TRUE,
keysize=1.5,
density.info=c("histogram","density","none"),
denscol=tracecol,
symkey=min(x<0,na.rm=TRUE)||symbreaks,
densadj=0.25,
#plotlabels
main=NULL,
xlab=NULL,
ylab=NULL,
#plotlayout
lmat=NULL,
lhei=NULL,
lwid=NULL,
#extras
...
)
Arguments
x
numericmatrixofthevaluestobeplotted.
Rowv
determinesifandhowthe row dendrogramshouldbereordered.Bydefault,itisTRUE,whichimpliesdendrogramiscomputedandreorderedbasedonrowmeans.IfNULLorFALSE,thennodendrogramiscomputedandnoreorderingisdone.Ifa dendrogram,thenitisused"as-is",iewithoutanyreordering.Ifavectorofintegers,thendendrogramiscomputedandreorderedbasedontheorderofthevector.
Colv
determinesifandhowthe column dendrogramshouldbereordered.Hastheoptionsasthe Rowv argumentaboveand additionally when x isasquarematrix, Colv="Rowv" meansthatcolumnsshouldbetreatedidenticallytotherows.
distfun
functionusedtocomputethedistance(dissimilarity)betweenbothrowsandcolumns.Defaultsto dist.
hclustfun
functionusedtocomputethehierarchicalclusteringwhen Rowv or Colv arenotdendrograms.Defaultsto hclust.
dendrogram
characterstringindicatingwhethertodraw'none','row','column'or'both'dendrograms.Defaultsto'both'.However,ifRowv(orColv)isFALSEorNULLanddendrogramis'both',thenawarningisissuedandRowv(orColv)argumentsarehonoured.
symm
logicalindicatingif x shouldbetreated symmetrically;canonlybetruewhen x isasquarematrix.
scale
characterindicatingifthevaluesshouldbecenteredandscaledineithertherowdirectionorthecolumndirection,ornone.Thedefaultis "row"if symm false,and "none" otherwise.
na.rm
logicalindicatingwhether NA'sshouldberemoved.
revC
logicalindicatingifthecolumnordershouldbe reversedforplotting,suchthate.g.,forthesymmetriccase,thesymmetryaxisisasusual.
add.expr
expressionthatwillbeevaluatedafterthecallto image.Canbeusedtoaddcomponentstotheplot.
breaks
(optional)Eitheranumericvectorindicatingthesplittingpointsforbinning x intocolors,oraintegernumberofbreakpointstobeused,inwhichcasethebreakpointswillbespacedequallybetween min(x) and max(x).
symbreaks
Booleanindicatingwhetherbreaksshouldbemadesymmetricabout0.Defaultsto TRUE ifthedataincludesnegativevalues,andto FALSE otherwise.
col
colorsusedfortheimage.Defaultstoheatcolors(heat.colors).
colsep,rowsep,sepcolor
(optional)vectorofintegersindicatingwhichcolumnsorrowsshouldbeseparatedfromtheprecedingcolumnsorrowsbyanarrowspaceofcolorsepcolor.
sepwidth
(optional)Vectoroflength2givingthewidth(colsep)orheight(rowsep)theseparatorboxdrawnbycolsepandrowsepasafunctionofthewidth(colsep)orheight(rowsep)ofacell.Defaultsto c(0.05,0.05)
cellnote
(optional)matrixofcharacterstringswhichwillbeplacedwithineachcolorcell,e.g.p-valuesymbols.
notecex
(optional)numericscalingfactorfor cellnote items.
notecol
(optional)characterstringspecifyingthecolorfor cellnote text.Defaultsto"green".
na.color
Colortouseformissingvalue(NA).Defaultstotheplotbackgroundcolor.
trace
characterstringindicatingwhetherasolid"trace"lineshouldbedrawnacross'row'sordown'column's,'both'or'none'.Thedistanceofthelinefromthecenterofeachcolor-cellisproportionaltothesizeofthemeasurement.Defaultsto'column'.
tracecol
characterstringgivingthecolorfor"trace"line.Defaultsto"cyan".
hline,vline,linecol
Vectorofvalueswithincellswhereahorizontalorverticaldottedlineshouldbedrawn.Thecolorofthelineiscontrolledby linecol.Horizontallinesareonlyplottedif trace is'row'or'both'.Verticallinesareonlydrawnif trace 'column'or'both'. hline and vline defaulttothemedianofthebreaks, linecol defaultstothevalueof tracecol.
margins
numericvectoroflength2containingthemargins(see par(mar=*))forcolumnandrownames,respectively.
ColSideColors
(optional)charactervectoroflength ncol(x) containingthecolornamesforahorizontalsidebarthatmaybeusedtoannotatethecolumnsof x.
RowSideColors
(optional)charactervectoroflength nrow(x) containingthecolornamesforaverticalsidebarthatmaybeusedtoannotatetherowsof x.
cexRow,cexCol
positivenumbers,usedas cex.axis infortheroworcolumnaxislabeling.Thedefaultscurrentlyonlyusenumberofrowsorcolumns,respectively.
labRow,labCol
charactervectorswithrowandcolumnlabelstouse;thesedefaultto rownames(x) or colnames(x),respectively.
key
logicalindicatingwhetheracolor-keyshouldbeshown.
keysize
numericvalueindicatingthesizeofthekey
density.info
characterstringindicatingwhethertosuperimposea'histogram',a'density'plot,ornoplot('none')onthecolor-key.
denscol
characterstringgivingthecolorforthedensitydisplayspecifiedby density.info,defaultstothesamevalueas tracecol.
symkey
Booleanindicatingwhetherthecolorkeyshouldbemadesymmetricabout0.Defaultsto TRUE ifthedataincludesnegativevalues,andto FALSEotherwise.
densadj
Numericscalingvaluefortuningthekernelwidthwhenadensityplotisdrawnonthecolorkey.(Seethe adjust parameterforthe density functionfordetails.)Defaultsto0.25.
main,xlab,ylab
main,x-andy-axistitles;defaultstonone.
lmat,lhei,lwid
visuallayout:
positionmatrix,columnheight,columnwidth.Seebelowfordetails
...
additionalargumentspassedonto image
Details
Ifeither Rowv or Colv aredendrogramstheyarehonored(andnotreordered).Otherwise,dendrogramsarecomputedas dd<-as.dendrogram(hclustfun(distfun(X))) where Xiseither x or t(x).
Ifeitherisavector(of“weights”)thentheappropriatedendrogramisreorderedaccordingtothesuppliedvaluessubjecttotheconstraintsimposedbythedendrogram,by reorder(dd,Rowv),intherowcase.Ifeitherismissing,asbydefault,thentheorderingofthecorrespondingdendrogramisbythemeanvalueoftherows/columns,i.e.,inthecaseofrows, Rowv<-rowMeans(x,na.rm=na.rm).Ifeitheris NULL, noreordering willbedoneforthecorrespondingside.
If scale="row" therowsarescaledtohavemeanzeroandstandarddeviationone.Thereissomeempiricalevidencefromgenomicplottingthatthisisuseful.
Thedefaultcolorsrangefromredtowhite(heat.colors)andarenotpretty.Considerusingenhancementssuchasthe RColorBrewer package, http:
//cran.r-project.org/src/contrib/PACKAGES.html#RColorBrewer toselectbettercolors.
Bydefaultfourcomponentswillbedisplayedintheplot.Atthetopleftisthecolorkey,toprightisthecolumndendogram,bottomleftistherowdendogram,bottomrightistheimageplot.WhenRowSideColororColSideColorareprovided,anadditionalroworcolumnisinsertedintheappropriatelocation.Thislayoutcanbeoverridenbyspecifiyingappropriatevaluesfor lmat, lwid,and lhei. lmat controlstherelativepostitionofeachelement,while lwid controlsthecolumnwidth,and lhei controlstherowheight.Seethehelppagefor layout fordetailsonhowtousethesearguments.
Value
Invisibly,alistwithcomponents
rowInd
rowindexpermutationvectorasreturnedby order.dendrogram.
colInd
columnindexpermutationvector.
call
thematchedcall
rowMeans,rowSDs
meanandstandarddeviationofeachrow:
onlypresentif scale="row"
colMeans,colSDs
meanandstandarddeviationofeachcolumn:
onlypresentif scale="column"
carpet
reorderedandscaled'x'valuesusedgeneratethemain'carpet'
rowDendrogram
rowdendrogram,ifpresent
colDendrogram
columndendrogram,ifpresent
breaks
valuesusedforcolorbreakpoints
col
colorsused
vline
center-linevalueusedforcolumntrace,presentonlyif trace="both" or trace="column"
hline
center-linevalueusedforrowtrace,presentonlyif trace="both" or trace="row"
colorTable
Athree-columndataframeprovidingthelowerandupperboundandcolorforeachbin
Note
Theoriginalrowsandcolumnsarereordered inanycase tomatchthedendrogram,e.g.,therowsby order.dendrogram(Rowv) where Rowv isthe(possibly reorder()ed)rowdendrogram.
heatmap.2() uses layout anddrawsthe image inthelowerrightcornerofa2x2layout.Consequentially,itcan not beused
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