Nothing
"plot.mat" <- plotMat <-
function(
x=M, #x should be a matrix or similar object
M=x, #M should be a matrix or similar object - both (x and M) are here to make the code compatible with generic plot and with older versions of plot.mat and possbily some other functions in the package
clu=NULL, #partition
ylab="",
xlab="",
main=NULL,
print.val=!length(table(M))<=2, #should the values be printed inside the cells
print.0=FALSE, #should the values equal to 0 be printed inside the cells, only used if 'print.val == TRUE'
plot.legend=!print.val&&!length(table(M))<=2, #should the legend for the colors be ploted
print.legend.val="out", #where should the values for the legend be printed: 'out' - outside the cells (bellow), 'in' - inside the cells, 'both' - inside and outside the cells
print.digits.legend=2, #the number of digits that should appear in the legend
print.digits.cells=2, #the number of digits that should appear in the cells (of the matrix and/or legend)
print.cells.mf=NULL, #if not null, the above argument is igonred, the cell values are printed as the cell are multiplied by this factor and rounded
outer.title=FALSE, #should the title be printed on the 'inner' or 'outer' plot, default is 'inner' if legend is ploted and 'outer' otherwise
title.line= ifelse(outer.title,-1.5,7), #the line (from the top) where the title should be printed
mar= c(0.5, 7, 8.5, 0)+0.1, #A numerical vector of the form 'c(bottom, left, top, right)' which gives the lines of margin to be specified on the four sides of the plot. The default is 'c(5, 4, 4, 2) + 0.1'.
cex.val="default", #size of the values printed
val.y.coor.cor = 0, #correction for centering the values in the sqares in y direction
val.x.coor.cor = 0, #correction for centering the values in the sqares in x direction
cex.legend=1, #size of the text in the legend,
legend.title="Legend", #the title of the legend
cex.axes="default", #size of the characters in axes, 'default' makes the cex so small that all categories can be printed
print.axes.val=NULL, #should the axes values be printed, 'default' prints each axis if 'rownames' or 'colnames' is not 'NULL'
print.x.axis.val=!is.null(colnames(M)), #should the x axis values be printed, 'default' prints each axis if 'rownames' or 'colnames' is not 'NULL'
print.y.axis.val=!is.null(rownames(M)), #should the y axis values be printed, 'default' prints each axis if 'rownames' or 'colnames' is not 'NULL'
x.axis.val.pos = 1.01, #y coordiante of the x axis values
y.axis.val.pos = -0.01, #x coordiante of the y axis values
cex.main=par()$cex.main,
cex.lab=par()$cex.lab,
yaxis.line=-1.5, #the position of the y axis (the argument 'line')
xaxis.line=-1, #the position of the x axis (the argument 'line')
legend.left=0.4,#how much left should the legend be from the matrix
legend.up=0.03, #how much left should the legend be from the matrix
legend.size=1/min(dim(M)), #relative legend size
legend.text.hor.pos=0.5, #horizontal position of the legend text (bottom) - 0 = bottom, 0.5 = middle,...
par.line.width = 3, #the width of the line that seperates the partitions
par.line.col = "blue", #the color of the line that seperates the partitions
IM.dens= NULL,
IM= NULL, #Image used for ploting (shaded lines)
wnet=NULL, #which net (if more) should be ploted - used if M is an array
wIM=NULL, #which IM (if more) should be used for ploting (defualt = wnet) - used if IM is an array
use.IM=length(dim(IM))==length(dim(M))|!is.null(wIM), #should IM be used for ploting?
dens.leg=c(null=100, nul=100),
blackdens=70,
plotLines = FALSE, #Should the lines in the matrix be printed (best set to FALSE for larger networks)
frameMatrix=TRUE, #Should the matrix be framed (if plotLines is FALSE)
x0ParLine=-0.1, #x coordinates for lines between row clusters
x1ParLine=1, #x coordinates for lines between row clusters
y0ParLine=0, #y coordinates for lines between col clusters
y1ParLine=1.1, #y coordinates for lines between col clusters
colByUnits=NULL, #a vector (of 0s and 1s) indicating whether ties of a unit should be marked with a diferent (nonblack) color - only used for binary networks
colByRow=NULL, #a vector (of 0s and 1s) indicating whether outgoing ties of a unit should be marked with a different (nonblack) color - only used for binary networks
colByCol=NULL, #a vector (of 0s and 1s) indicating whether incoming ties of a unit should be marked with a different (nonblack) color - only used for binary networks
mulCol = 2,
joinColOperator = "+",
colTies=FALSE,
maxValPlot=NULL, # maximal value used for determining the color of cells in the plot. This value and all higher (in absolute terms) will produce a pure black/red color
printMultipliedMessage = TRUE, # shold mutiplication message be printed when values were the printed tie values are multiplied
replaceNAdiagWith0=TRUE, #Should the diagonal with only NAs be replace by 0s?
... #aditional arguments to plot.default
){
old.mar<-par("mar")
if(length(dim(IM))>2&use.IM){
if(is.null(wIM))wIM<-wnet
if(is.null(wIM)) wIM<-1
IM<-IM[wIM,,]
}
tempClu<-clu
if(length(dim(M))>2){
if(!is.null(wnet)){
relDim<-which.min(dim(M))
if(relDim==1){
M<-M[wnet,,]
}else if(relDim==1){
M<-M[,,wnet]
}else stop("More than 2 dimensions where relation dimension can not be determined")
}else{
plot.array(M = M,
clu=tempClu, #partition
ylab=ylab,
xlab=xlab,
main.title=main,main.title.line=-2,
print.val=print.val, #should the values be printed inside the cells
print.0=print.0, #should the values equal to 0 be printed inside the cells, only used if 'print.val == TRUE'
plot.legend=plot.legend, #should the legend for the colors be ploted
print.legend.val=print.legend.val, #where should the values for the legend be printed: 'out' - outside the cells (bellow), 'in' - inside the cells, 'both' - inside and outside the cells
print.digits.legend=print.digits.legend, #the number of digits that should appear in the legend
print.digits.cells=print.digits.cells, #the number of digits that should appear in the cells (of the matrix and/or legend)
print.cells.mf=print.cells.mf, #if not null, the above argument is igonred, the cell values are printed as the cell are multiplied by this factor and rounded
outer.title=outer.title, #should the title be printed on the 'inner' or 'outer' plot, default is 'inner' if legend is ploted and 'outer' otherwise
title.line= title.line, #the line (from the top) where the title should be printed
mar= mar, #A numerical vector of the form 'c(bottom, left, top, right)' which gives the lines of margin to be specified on the four sides of the plot. The default is 'c(5, 4, 4, 2) + 0.1'.
cex.val=cex.val, #size of the values printed
val.y.coor.cor = val.y.coor.cor, #correction for centering the values in the sqares in y direction
val.x.coor.cor = val.x.coor.cor, #correction for centering the values in the sqares in x direction
cex.legend=cex.legend, #size of the text in the legend,
legend.title=legend.title, #the title of the legend
cex.axes=cex.axes, #size of the characters in axes, 'default' makes the cex so small that all categories can be printed
print.axes.val=print.axes.val, #should the axes values be printed, 'default' prints each axis if 'rownames' or 'colnames' is not 'NULL'
print.x.axis.val=print.x.axis.val, #should the x axis values be printed, 'default' prints each axis if 'rownames' or 'colnames' is not 'NULL'
print.y.axis.val=print.y.axis.val, #should the y axis values be printed, 'default' prints each axis if 'rownames' or 'colnames' is not 'NULL'
x.axis.val.pos = x.axis.val.pos, #y coordiante of the x axis values
y.axis.val.pos = y.axis.val.pos, #x coordiante of the y axis values
cex.main=cex.main,
cex.lab=cex.lab,
yaxis.line=yaxis.line, #the position of the y axis (the argument 'line')
xaxis.line=xaxis.line, #the position of the x axis (the argument 'line')
legend.left=legend.left,#how much left should the legend be from the matrix
legend.up=legend.up, #how much left should the legend be from the matrix
legend.size=legend.size, #relative legend size
legend.text.hor.pos=legend.text.hor.pos, #horizontal position of the legend text (bottom) - 0 = bottom, 0.5 = middle,...
par.line.width = par.line.width , #the width of the line that seperates the partitions
par.line.col = par.line.col, #the color of the line that seperates the partitions
IM.dens= IM.dens,
IM= IM, #Image used for ploting (shaded lines)
wIM=wIM, #which IM (if more) should be used for ploting (defualt = wnet) - used if IM is an array
use.IM=use.IM, #should IM be used for ploting?
dens.leg=dens.leg,
blackdens=blackdens,
plotLines = plotLines,...
)
return(invisible(NULL))
}
}
dm<-dim(M)
if(class(M)!="matrix"&&class(M)!="mat"){
pack<-attr(class(M),"package")
if(!(is.null(pack))&&pack=="Matrix"){
if(requireNamespace("Matrix")){
M<-as.matrix(M)
} else stop("The supplied object needs Matrix packege, but the package is not available (install it!!!).")
} else {
warning("Attempting to convert object of class ",class(M)," to class 'matrix'. Keep fingers crossed.")
M<-as.matrix(M)
}
}
if(replaceNAdiagWith0 & all(is.na(diag(M)))) diag(M)<-0
if(is.null(main)){
objName<-deparse(substitute(M))
if(objName[1]=="x"){
objName<-deparse(substitute(x))
}
if(length(objName)>1) objName=""
main <- paste("Matrix",objName)
if(nchar(main)>50) main<-substr(main,1,50)
}
#if(length(main)>26)
if(is.logical(print.axes.val)){
print.x.axis.val<-print.y.axis.val<-print.axes.val
}
#defining text on the axes if row or colnames do not exist
if(is.null(rownames(M))){
rownames(M)<-1:dm[1]
}
if(is.null(colnames(M))){
colnames(M)<-1:dm[2]
}
if(!is.null(clu)){ #is any clustering provided, ordering of the matrix if 'TRUE'
if(!is.list(clu)){
tclu<-table(clu)
or.c<-or.r<-order(clu)
clu<-list(clu,clu)
lines.col<-cumsum(tclu)[-length(tclu)]*1/dm[2]
lines.row<-1-lines.col
}else if(is.list(clu)&&length(clu)==2){
if(!is.null(clu[[1]])){
tclu.r<-table(clu[[1]])
or.r<-order(clu[[1]])
lines.row<- 1-cumsum(tclu.r)[-length(tclu.r)]*1/dm[1]
} else{
or.r<-1:dim(M)[1]
lines.row<-NULL
}
if(!is.null(clu[[2]])){
tclu.c<-table(clu[[2]])
or.c<-order(clu[[2]])
lines.col<-cumsum(tclu.c)[-length(tclu.c)]*1/dm[2]
} else{
or.c<-1:dim(M)[2]
lines.col<-NULL
}
} else stop("Networks with more that 2 modes (ways) must convert to 1-mode networks before it is sent to this function.")
M<-M[or.r,or.c]
clu<-lapply(clu,function(x)as.numeric(factor(x)))
}
if(is.null(IM.dens)){
if(!is.null(IM)&use.IM){
IM.dens<-matrix(-1,ncol=dim(IM)[2],nrow=dim(IM)[1])
for(i in names(dens.leg)){
IM.dens[IM==i]<- dens.leg[i]
}
}
}
if(!is.null(IM.dens)){
dens<-matrix(-1,nrow=dm[1], ncol=dm[2])
for(i in unique(clu[[1]])){
for(j in unique(clu[[2]])){
dens[clu[[1]]==i,clu[[2]]==j]<-IM.dens[i,j]
}
}
dens<-dens[or.r,or.c]
}
if(cex.axes=="default"){ #defining the size of text on the axes
cex.x.axis<-min(15/dm[2],1)
cex.y.axis<-min(15/dm[1],1)
}else{
cex.x.axis<-cex.axes
cex.y.axis<-cex.axes
}
#defining text on the axes
yaxe<-rownames(M)
xaxe<-colnames(M)
ytop <- rep(x=(dm[1]:1)/dm[1],times=dm[2]) #definin the positions of rectangules
ybottom<- ytop - 1/dm[1]
xright <- rep(x=(1:dm[2])/dm[2],each=dm[1])
xleft <- xright - 1/dm[2]
if(all(M %in% c(0,1))){
# browser()
mulCol<-mulCol
if(is.null(colByRow)&is.null(colByCol)) {
colByRow<-colByCol<-colByUnits
} else {
if(is.null(colByRow)){
colByRow<-rep(0, length(colByCol))
mulCol<-1
}
if(is.null(colByCol)){
colByCol<-rep(0, length(colByRow))
}
colByUnits<-TRUE
}
col<-M
if(all(col %in% c(0,1))& (!is.null(colByUnits))){
newCol<-outer(colByRow,colByCol*mulCol,FUN=joinColOperator)
if(!is.null(clu)) newCol<-newCol[or.r,or.c]
if(colTies){
col[M>0]<-col[M>0]+newCol[M>0]
}else{
newCol[newCol>0]<-newCol[newCol>0]+1
col[M==0]<-col[M==0]+newCol[M==0]
}
}
} else {
aM<-abs(M)
if(!is.null(maxValPlot)){
aM[aM>maxValPlot]<-maxValPlot
}
max.aM<-max(aM)
aMnorm<-as.vector(aM)/max.aM
if(max.aM!=0){
col<-grey(1-aMnorm) #definin the color of rectangules
}else col<-matrix(grey(1),nrow=dm[1],ncol=dm[2])
col[M<0]<-paste("#FF",substr(col[M<0],start=4,stop=7),sep="")
}
asp<-dm[1]/dm[2] #making sure that the cells are squares
par(mar=mar, xpd=NA) #ploting
plot.default(c(0,1),c(0,1),type="n",axes=FALSE,ann=FALSE,xaxs="i",asp=asp,...)
if(is.null(IM.dens)||all(IM.dens==-1)){
rect(xleft=xleft, ybottom=ybottom, xright=xright, ytop=ytop, col=col,cex.lab=cex.lab,border=if(plotLines)"black" else NA)
}else{
rect(xleft=xleft, ybottom=ybottom, xright=xright, ytop=ytop, col=col,cex.lab=cex.lab,density=dens,border=if(plotLines)"black" else NA)
}
if(frameMatrix) rect(xleft=0, ybottom=0, xright=1, ytop=1, cex.lab=cex.lab,border="black")
if(!is.null(clu)){ #ploting the lines between clusters
if(!is.null(lines.row)) segments(x0=x0ParLine,x1=x1ParLine,y0=lines.row,y1=lines.row,col=par.line.col,lwd=par.line.width)
if(!is.null(lines.col)) segments(y0=y0ParLine,y1=y1ParLine,x0=lines.col,x1=lines.col,col=par.line.col,lwd=par.line.width )
}
if(print.y.axis.val) text(x=y.axis.val.pos, y = (dm[1]:1)/dm[1]-1/dm[1]/2 +val.y.coor.cor,labels = yaxe,cex=cex.y.axis,adj=1)
if(print.x.axis.val) text(y=x.axis.val.pos, x = (1:dm[2])/dm[2]-1/dm[2]/2 +val.x.coor.cor, srt=90, labels = xaxe, cex=cex.x.axis,adj=0)
title(outer=outer.title,ylab=ylab,xlab=xlab,main=main, line=title.line,cex.main=cex.main)
if(print.val){ #ploting the values in the cells if selected
norm.val<-as.vector(M)/max(abs(M))
aMnorm<-abs(norm.val)
col.text<-1-round(aMnorm)
if(!print.0) col.text[as.vector(M)==0]<-0
if(length(table(col.text))==2) {
col.labels<-c("white","black")
} else col.labels<-c("white")
col.text<-as.character(factor(col.text,labels=col.labels))
if(!is.null(IM.dens)&&!all(IM.dens==-1)) col.text[col.text=="white"&dens>0&dens<blackdens]<-"black"
col.text[col.text=="black"&norm.val<0]<-"red"
if(!print.0) col.text[as.vector(M)==0]<-"transparent"
maxM<-formatC(max(M),format="e")
if(is.null(print.cells.mf)){
if(all(trunc(M)==M)& max(M)<10^print.digits.cells){
multi<-1
}else{
multi<-floor(log10(max(M)))
multi<-(multi-(print.digits.cells - 1))*(-1)
multi<-10^multi
}
}else multi <- print.cells.mf
M.plot<-round(M*multi)
text(x=(xleft+xright)/2+val.x.coor.cor,y=(ytop+ybottom)/2+val.y.coor.cor, labels=as.vector(M.plot),col=col.text,cex=ifelse(cex.val=="default",min(10/max(dm),1),cex.val))
if(multi!=1 & printMultipliedMessage) mtext(text=paste("* all values in cells were multiplied by ",multi,sep=""),side=1, line=-0.7,cex=0.70)
}
if(plot.legend){ #ploting the legend if selected
if(asp>=1){
xright.legend<- -legend.left
xleft.legend <- xright.legend - 1*legend.size*asp
ybottom.legend <- 1+(4:0)*legend.size+ legend.up
ytop.legend <- ybottom.legend + 1*legend.size
}else{
xright.legend<- -legend.left
xleft.legend <- xright.legend - 1*legend.size
ybottom.legend <- 1+(4:0)*legend.size*asp+ legend.up
ytop.legend <- ybottom.legend + 1*legend.size*asp
}
col.legend<-gray(4:0/4)
rect(xleft=xleft.legend, ybottom=ybottom.legend, xright=xright.legend, ytop=ytop.legend, col=col.legend)
if(print.legend.val=="out"|print.legend.val=="both") text(x=xright.legend + 1/20,y= (ytop.legend+ybottom.legend)/2, labels=formatC(0:4/4*max(M), digits = print.digits.legend,format="g"),adj=0,cex=cex.legend)
text(x=xleft.legend,y=ytop.legend[1] + legend.size/asp/2+0.02, labels=legend.title,font=2,cex=cex.legend,adj=0)
if(print.legend.val=="in"|print.legend.val=="both"){
col.text.legend<-round(4:0/4)
if(!print.0) col.text.legend[1]<-0
col.text.legend<-as.character(factor(col.text.legend,labels=c("white","black")))
if(!print.val){
if(is.null(print.cells.mf)){
if(all(trunc(M)==M)& max(M)<10^print.digits.cells){
multi<-1
}else{
multi<-floor(log10(max(M)))
multi<-(multi-(print.digits.cells - 1))*(-1)
multi<-10^multi
}
}else multi <- print.cells.mf
maxM<-round(max(M)*multi)
} else maxM<-max(M.plot)
text(x=(xleft.legend+xright.legend)/2,y=(ytop.legend+ybottom.legend)/2, labels=round(0:4/4*maxM),col=col.text.legend,cex=cex.legend)
}
}
par(mar=old.mar)
}
"plot.array" <- plotArray <-
function(
x=M, #x should be a matrix or similar object
M=x, #M should be a matrix or similar object - both (x and M) are here to make the code compatible with generic plot and with older versions of plot.mat and possbily some other functions in the package
..., #aditional arguments to plot.mat
main.title=NULL,main.title.line=-2,mfrow=NULL
){
if(is.null(main.title)){
objName<-deparse(substitute(M))
if(objName=="x")objName<-deparse(substitute(x))
main.title <- paste("Matrix",objName)
if(nchar(main.title)>50) main.title<-substr(main.title,1,50)
}
dM<-dim(M)
relDim<-which.min(dM)
nDim<-dM[relDim]
if(is.null(mfrow)|(prod(mfrow)<nDim)){
if(nDim<4){
mfrow<-c(1,nDim)
} else if(nDim<6){
mfrow<-c(2,ceiling(nDim/2))
} else{
nr<-round(sqrt(nDim/6)*2); nc<-ceiling(nDim/nr)
mfrow<-c(nr,nc)
}
}
par.def<-par(no.readonly = TRUE)
par(mfrow=mfrow)
relNames<-dimnames(M)[[relDim]]
if(is.null(relNames)) relNames<-1:nDim
for(iName in relNames) {
if(relDim==1){
plot.mat(M[iName,,],main=iName,...)
} else if(relDim==3) plot.mat(M[,,iName],main=iName,...)
}
title(main=main.title,outer=TRUE,line=main.title.line)
par(par.def)
}
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