R/plotMatrix.R

In Umatrix: Visualization of Structures in High-Dimensional Data

plotMatrix <- function(Matrix = NULL, BestMatches=NULL, Cls = NULL, ClsColors=NULL,
                        ColorStyle = "Umatrix", Toroid=TRUE,BmSize=2, DrawLegend=F,
                        FixedRatio=T, CutoutPol=NULL, Nrlevels = NULL, TransparentContours = T,
                        Imx = NULL, Clean=F, RemoveOcean=F, TransparentOcean = FALSE,
                        Title = NULL, BestMatchesLabels = NULL,
                        BestMatchesLabelStyle = c(), BestMatchesShape=19, MarkDuplicatedBestMatches = F, YellowCircle = F){


 if(is.null(ClsColors)) ClsColors=DefaultColorSequence()
 if(ColorStyle == "Umatrix") Colormap = c("#3C6DF0","#3C6DF0","#3C6DF0","#006602","#006A02","#006D01","#007101","#007501","#007901","#007C00","#008000","#068103","#118408","#0B8305","#17860A","#1D870D","#228810","#288A12","#2E8B15","#348D18","#398E1A","#3F8F1D","#45911F","#4A9222","#509325","#569527","#5C962A","#61982C","#67992F","#6D9A32","#729C34","#789D37","#7E9F39","#84A03C","#89A13F","#8FA341","#95A444","#9AA547","#A0A749","#A6A84C","#ACAA4E","#B1AB51","#B7AC54","#BDAE56","#C3AF59","#C8B15B","#CEB25E","#CBAF5C","#C8AC59","#C5A957","#C3A654","#C0A352","#BDA050","#BA9D4D","#B7994B","#B49648","#B29346","#AF9044","#AC8D41","#A98A3F","#A6873C","#A3843A","#A08138","#9E7E35","#9B7B33","#987830","#95752E","#92722B","#8F6E29","#8C6B27","#8A6824","#876522","#84621F","#815F1D","#7E5C1B","#7B5918","#795616","#765313","#714E0F","#6C480B","#674307","#6F4D15","#785822","#806230","#896D3E","#91774C","#998159","#A28C67","#AA9675","#B3A183","#BBAB90","#C3B59E","#CCC0AC","#D4CABA","#DDD5C7","#E5DFD5","#E7E1D8","#E9E4DB","#EBE6DE","#ECE8E1","#EEEAE4","#F0EDE7","#F2EFEA","#F4F1ED","#F6F4F0","#F8F6F3","#F9F8F6","#FBFAF9","#FDFDFC","#FFFFFF","#FFFFFF","#FEFEFE","#FEFEFE","#FEFEFE","#FDFDFD","#FDFDFD","#FDFDFD","#FCFCFC","#FCFCFC","#FCFCFC","#FBFBFB","#FBFBFB","#FBFBFB","#FAFAFA","#FAFAFA","#FAFAFA","#F9F9F9","#F9F9F9","#FFFFFF","#FFFFFF")
 else if(ColorStyle == "Pmatrix") Colormap = c("#FFFFFF","#FFFFF7","#FFFFEF","#FFFFE7","#FFFFDF","#FFFFD7","#FFFFCF","#FFFFC7","#FFFFBF","#FFFFB7","#FFFFAF","#FFFFA7","#FFFF9F","#FFFF97","#FFFF8F","#FFFF87","#FFFF80","#FFFF78","#FFFF70","#FFFF68","#FFFF60","#FFFF58","#FFFF50","#FFFF48","#FFFF40","#FFFF38","#FFFF30","#FFFF28","#FFFF20","#FFFF18","#FFFF10","#FFFF08","#FFFF00","#FFFA00","#FFF400","#FFEF00","#FFEA00","#FFE400","#FFDF00","#FFDA00","#FFD400","#FFCF00","#FFCA00","#FFC500","#FFBF00","#FFBA00","#FFB500","#FFAF00","#FFAA00","#FFA500","#FF9F00","#FF9A00","#FF9500","#FF8F00","#FF8A00","#FF8500","#FF8000","#FF7A00","#FF7500","#FF7000","#FF6A00","#FF6500","#FF6000","#FF5A00","#FF5500","#FF5000","#FF4A00","#FF4500","#FF4000","#FF3A00","#FF3500","#FF3000","#FF2B00","#FF2500","#FF2000","#FF1B00","#FF1500","#FF1000","#FF0B00","#FF0500","#FF0000","#FA0000","#F40000","#EF0000","#EA0000","#E40000","#DF0000","#DA0000","#D40000","#CF0000","#CA0000","#C50000","#BF0000","#BA0000","#B50000","#AF0000","#AA0000","#A50000","#9F0000","#9A0000","#950000","#8F0000","#8A0000","#850000","#800000","#7A0000","#750000","#700000","#6A0000","#650000","#600000","#5A0000","#550000","#500000","#4A0000","#450000","#400000","#3A0000","#350000","#300000","#2B0000","#250000","#200000","#1B0000","#150000","#100000","#0B0000","#050000")
 else if(ColorStyle == "Empty") Colormap = rep("white", 100)
 else stop("ColorStyle not found.")

# if(!is.null(Imx)) Imx = Imx[nrow(Imx):1,]


# v <- plotMatrix()
# Draws a plot of given Umatrix
# INPUT
# OPTIONAL
# Umatrix(1:Lines,1:Columns)	      Umatrix to be plotted
# BestMatches(1:n,1:2)		      Positions of bestmatches to be plotted onto the Umatrix
# Cls(1:n)			        Class identifier for the bestmatch at the given point
# ClsColors(1:m)			Vector of colors that will be used to colorize the different classes
# Colormap(1:o)				Vector of colors that will be used to colorize the Heights of the Umatrix
# BmSize                Integer between 0.1 and 5, magnification factor of the points,
#                       if BestMatches given
# DrawLegend
# FixedRatio            should the ratio of Width and Height be fixed or matched to the window Width and Height
# CutoutPol(1:n,1:2)     only draws the area within given polygon
# Nrlevels               nr of breaks that will be done
# TransparentContours    use half transparent contours. Looks better but is slow
# Imx                    a Imx (Imx) that will be used to cut out the umatrix
# Fast                  Faster version that will be drawn using baseplot
# RemoveOcean             restrict the umatrix to the island, and reduce the ocean to a minimum
# TransparentOcean        draw the water surrounding the island transparent instead of blue
# Title                   a title to be printed above the umatrix
# BestMatchesLabels(1:n)         a vector of strings matching to the bestmatches, that will be shown above the bestmatches
# BestMatchesLabelStyle           a list containing possible modifications to the style of the labels
# BestMatchesShape                number of the R-Shape to be used for drawing BMU
# MarkDuplicatedBestMatches
# YellowCircle            draw a circle around bestmatches to get a better contrast

# OUTPUT
# ---()
# author: Florian Lerch
# 1.Editor: MT 09/2015 BmSize added, NumberContours added, region=T set
# 2.Editor: MT 04/2016: Umatrix-Normierung, Definition der Hoehen im topview

  #library(reshape2) # necessary for "melt" which converts the Umatrix to a data.frame
  #library(ggplot2)
  #library(fields)

  # in einer frueheren Variante wurden BestMatches mit der groesse 2 wesentlich kleiner gezeichnet. diese proportionen
  # werden hiermit aufrechterhalten.
  BmSize = BmSize / 2

  ################
  #### bmuLabel Standard Style
  ################
  if(is.null(BestMatchesLabelStyle$color)) BestMatchesLabelStyle$color = "white"
  if(is.null(BestMatchesLabelStyle$fontface)) BestMatchesLabelStyle$fontface = "bold"
  if(is.null(BestMatchesLabelStyle$fill)) BestMatchesLabelStyle$fill = "red"
  if(is.null(BestMatchesLabelStyle$alpha)) BestMatchesLabelStyle$alpha = 0.5
  if(is.null(BestMatchesLabelStyle$angle)) BestMatchesLabelStyle$angle = 0
  if(is.null(BestMatchesLabelStyle$size)) BestMatchesLabelStyle$size = 4
  if(is.null(BestMatchesLabelStyle$nudge_x)) BestMatchesLabelStyle$nudge_x = 0
  if(is.null(BestMatchesLabelStyle$nudge_y)) BestMatchesLabelStyle$nudge_y = 2

  if(!Toroid){
    Imx = NULL
    RemoveOcean = FALSE
    TransparentOcean = FALSE
  }

  #########
  #########

  if(is.null(Matrix))
    stop("Matrix needs to be given")

  if(!is.matrix(Matrix)){
    stop("Matrix has to be of type matrix")
  }
  if(length(dim(Matrix))!=2)
    stop("Matrix has to be a of type matrix, not an array")

  if(!is.null(Cls)){
    if(length(ClsColors) < length(DefaultColorSequence()))
      ClsColors = c(ClsColors, DefaultColorSequence()[(length(ClsColors)+1):(length(DefaultColorSequence()))])
    if(max(Cls) > length(ClsColors))
      stop(paste("The amount of given Colors (ClsColors) is not enough for the Cls. The highest Cls Value is",
                 max(Cls),"while the number of ClsColors only reaches to",
                 length(ClsColors)))
  }

## MT: Normalization der Umatrix werte
  # Milligan, Copper 1988 A Study of Standadization of Variables in Cluster Analysis,
  # robust Normalization Z_5 :"Z_5 is bounded by 0.0 and 1.0 with at least one observed value at each of these end points"
  quants=quantile(as.vector(Matrix),c(0.01,0.5,0.99),na.rm = T)
  # minU=min(Umatrix,na.rm=T)
  # maxU=max(Umatrix,na.rm=T)
  minU=quants[1]
  maxU=quants[3]
  #Verhaeltnis zwischen minhoehe/maxHoehe=1/HeightScale

  Matrix=(Matrix-minU)/(maxU-minU)

  quants2=quantile(as.vector(Matrix),c(0.01,0.5,0.99),na.rm = T)
  minU2=quants2[1]
  maxU2=quants2[3]

  ### Hoehe aus Umatrix schaetzen
  #Verhaeltnis zwischen minhoehe/maxHoehe=1/HeightScale
  if(is.null(Nrlevels)){
    Nrlevels=round(maxU2/max(minU2,0.05),0)
  }
#MT: Die Level muessen vor der Begrenzung der Werte auf 0 und 1 gesetz werden,
#aber nachdem der Wertebereich umgeschoben wurde, damit die Dichte in den Grenzbereichen abgeschetzt werden kann
  indMax=which(Matrix>1,arr.ind=T)
  indMin=which(Matrix<0,arr.ind=T)

  if(length(indMax)>0)
    Matrix[indMax]=1
  if(length(indMin)>0)
    Matrix[indMin]=0



  #print(maxU2)
  #print(Nrlevels)

  BestMatches = CheckBestMatches(BestMatches, Cls)
  CheckUmatrix(Matrix, shiny=F)
  CheckImx(Imx, shiny=F)


  # force rownames. this keeps log of the "original position" of the bestmatch within the list.
  # that is necessary because of the way BestMatchesLabels is currently defined.
  if(!is.null(BestMatches)){
    if(is.null(rownames(BestMatches))) rownames(BestMatches) <- 1:nrow(BestMatches)
  }

  # verknuepfe BestMatchesLabels mit BestmatchKey
  if((!is.null(BestMatches)) & (!is.null(BestMatchesLabels))){
    BestMatchesLabels <- cbind(BestMatches[,1], BestMatchesLabels)
  }

  Nrlevels2=Nrlevels #nicht konturen sondern farbintervalle!
  #lohnt sich nicht eine andere zahl als die die konturenanzahl zu setzen
  # get Toroid values for the Umatrix
  if(Toroid){
    tU <- ToroidUmatrix(Matrix, BestMatches, Cls)
    Matrix <- tU$Umatrix
    BestMatches <- tU$BestMatches
    Cls <- tU$Cls
  }
  #else if(!is.null(Imx)){ # Imxen beziehen sich auf 16 fache kachelung
  #  tU <- ToroidUmatrix(Umatrix, BestMatches, Cls)
  #  tU <- ToroidUmatrix(tU$Umatrix, tU$BestMatches, tU$Cls)
  #  Umatrix <- tU$Umatrix
  #  BestMatches <- tU$BestMatches
  #  Cls <- tU$Cls
  #}

  # configure filter, so that every bestmatch stays in
  if(!is.null(BestMatches)){
    BestMatchesFilter = rep(T,nrow(BestMatches)) # every Bestmatch stays
  }

  # put Imx on Umatrix and bestmatches if given
  if(!is.null(Imx)){
    for(i in 1:nrow(Imx)){
      for(j in 1:ncol(Imx)){
        if(Imx[i,j] == 1){
          Matrix[i,j] = NA
          if(!is.null(BestMatches))
            BestMatchesFilter[(BestMatches[,2] == i) & (BestMatches[,3] == j)] = F
        }
      }
    }

    if(!is.null(BestMatches)) BestMatches = BestMatches[BestMatchesFilter,]
    if((!is.null(Cls)) & (!is.null(BestMatches))) Cls = Cls[BestMatchesFilter]
  }

  #### remove ocean around Umatrix
  if(RemoveOcean){
    oceanLine = !apply(Matrix, 1, function(x) any(x != -1))
    startLine = min(which(!oceanLine),na.rm=T)
    endLine = length(oceanLine) - min(which(rev(!oceanLine)),na.rm=T) + 1

    oceanCol = !apply(Matrix, 2, function(x) any(x != -1))
    startCol = min(which(!oceanCol),na.rm=T)
    endCol = length(oceanCol) - min(which(rev(!oceanCol)),na.rm=T) + 1

    if(!is.null(BestMatches)){
      BestMatches <- BestMatches - cbind(rep(0,nrow(BestMatches)),startLine-1,startCol-1)
    }
    Matrix <- Matrix[startLine:endLine,startCol:endCol]
  }

  if(!TransparentOcean) Matrix[which(is.na(Matrix))] = 0

  nrows = nrow(Matrix)
  ncols = ncol(Matrix)

  colorx = Colormap

  # define level intervals
  # 35 levels
  # upper limit a bit above 1 so that every point inside the Umatrix is below it
  levelBreaks <- seq(0,1.000001,length.out=(Nrlevels2+1))

  # change Umatrix into 35 fixed values
  unfixedMatrix <- Matrix
  for(i in 1:Nrlevels2){
    Matrix[ (Matrix >= levelBreaks[i]) & (Matrix <= levelBreaks[i+1]) ] = levelBreaks[i]
  }

  #testUmatrix = Umatrix[which(is.na(Umatrix))] = 0

  # cut out polygon out of Umatrix
  #if(!is.null(CutoutPol)){
  #  UmatrixPolygon <- in.poly(dfUmatrix[,c(2,1)],CutoutPol)
  #  dfUmatrix <- dfUmatrix[UmatrixPolygon,]
  #  if(!is.null(BestMatches)){
  #    BestMatchesPolygon <- in.poly(BestMatches[,c(3,2)], CutoutPol)
  #    BestMatches <- BestMatches[BestMatchesPolygon,]
  #    if(!is.null(Cls)) Cls <- Cls[BestMatchesPolygon]
  #  }
  #}


  duplicatedBestMatches = matrix(,ncol=2, nrow=0)
  # find duplicated bestmatches
  if(!is.null(BestMatches)){
    dup = duplicated(BestMatches[,1], fromLast = T) | duplicated(BestMatches[,1])
    duplicatedBestMatches = BestMatches[dup,,drop=F]
  }

  # transparency of the contours
  if(TransparentContours) alpha = 0.5
  else alpha = 1

  ###############
  # draw the Umatrix with ggplot
  ###############
  #### convert Umatrix into a dataframe
  unnamedMatrix <- Matrix
  colnames(unnamedMatrix) <- NULL
  rownames(unnamedMatrix) <- NULL

  dfMatrix <- melt(unnamedMatrix)
  colnames(dfMatrix) <- c("y","x","z")

  dfMatrix2 = dfMatrix
  dfMatrix2[is.na(dfMatrix$z),3]=0

  MatrixPlot <- ggplot(dfMatrix, aes_string('x','y')) +   # data layer
  #stat_contour(geom="polygon", aes(fill=..level..,z=z, colour=..level..),binWidth=0.05)+
  geom_tile(aes_string(fill = 'z'))+

  scale_fill_gradientn(colours=colorx,space='Lab', na.value="transparent")+
  stat_contour(aes_string(z='z'), data=dfMatrix2,bins=Nrlevels,size = 0.25,color='black',alpha=alpha,na.rm = F)+ #80% der Laufzeit wird fuer konturen benoetigt
  ylab("Lines (y)")+xlab("Columns (x)")

  #MatrixPlot = MatrixPlot


  if(!DrawLegend) MatrixPlot <- MatrixPlot + theme(legend.position="none")

  if(FixedRatio)
    MatrixPlot <- MatrixPlot + coord_fixed(1,xlim=c(0.5,ncols+0.5),ylim=c(nrows+0.5,0.5), expand=0)#c(0.5,nrows+0.5), expand = 0)#+ coord_trans(y='reverse')# + scale_y_reverse()
  else
    MatrixPlot <- MatrixPlot + coord_cartesian(xlim=c(0.5,ncols+0.5),ylim=c(nrows+0.5,0.5), expand=0)#c(nrows+0.5,0.5), expand = 0)#+coord_trans(y='reverse')# + scale_y_reverse()

  if(Clean){
    if(is.null(Title)){
      MatrixPlot <- MatrixPlot + theme(
                                          axis.ticks = element_blank(),
                                          axis.text = element_blank(),
                                          axis.ticks.length = unit(0.01,"lines"),
                                          #axis.text.margin = unit(0,"null"),
                                          panel.grid = element_blank(),
                                          axis.title.x=element_blank(),
                                          plot.margin = unit( c(0.001,0.001,0.001,0.001) , "lines" ),
                                          axis.title.y=element_blank(),
                                          panel.grid.major = element_blank(),
                                          panel.grid.minor = element_blank(),

                                          panel.background = element_blank(),
                                          #plot.background = element_blank(),
                                          legend.background = element_blank(),
                                          panel.border = element_blank(),
                                          plot.background=element_rect(fill="white", colour=NA)

                                          ) + labs('x'=NULL, 'y'=NULL)

	#if(packageVersion("ggplot2") >= 2.2.1) UmatrixPlot <- UmatrixPlot + theme(panel.spacing = unit(0,"null"))
	MatrixPlot <- MatrixPlot +theme(panel.spacing = unit(0,"null"))
    }
    else{
      MatrixPlot <- MatrixPlot + theme(
        axis.ticks = element_blank(),
        axis.text = element_blank(),
        axis.ticks.length = unit(0.01,"lines"),
        #axis.text.margin = unit(0,"null"),
        #panel.grid = element_blank(),
        #panel.margin = unit(0,"null"),
        axis.title.x=element_blank(),
        #plot.margin = unit( c(0.001,0.001,0.001,0.001) , "lines" ),
        axis.title.y=element_blank(),
        #panel.grid.major = element_blank(),
        #panel.grid.minor = element_blank(),

        panel.background = element_blank(),
        #plot.background = element_blank(),
        legend.background = element_blank(),
        panel.border = element_blank(),
        plot.background=element_rect(fill="white", colour=NA)

      ) + labs('x'=NULL, 'y'=NULL)
    }
  }

  # add the BestMatches
  if(!is.null(BestMatches)){
    if(is.null(Cls)) Cls <- rep(1,nrow(BestMatches))

    Cls = factor(Cls)
    #classes <- sort(na.last=T,c(unique(Cls), setdiff(1:100,unique(Cls))))

    uniqueClasses <- sort(na.last=T,unique(Cls))

    ClsColors = c("darkgreen", ClsColors)
    names(ClsColors) = 0:(length(ClsColors)-1)

    MatrixPlot = MatrixPlot+scale_color_manual(values=ClsColors, name="Clusters")
    #UmatrixPlot = UmatrixPlot+scale_color_manual(c("0"="blue", "1"="green", "2"="red", "3"="yellow", "4"="brown", "5"="black",
    #                                               "6"="magenta", "7" = "white"), name="Clusters")

    if(!is.null(BestMatchesShape))
      if(length(BestMatchesShape)>1)
        MatrixPlot = MatrixPlot+scale_shape_manual(values=BestMatchesShape, name="Clusters")

    # extract bestmatches without a class
    d = data.frame(y = BestMatches[,2], x = BestMatches[,3], class = Cls)
    #d1 = data.frame(y = BestMatches[Cls!=0,2], x = BestMatches[Cls!=0,3], class = Cls[Cls!=0])
    #d2 = data.frame(y = BestMatches[Cls==0,2], x = BestMatches[Cls==0,3], class = rep(length(ClsColors),sum(Cls==0)))

    if(YellowCircle)
      MatrixPlot <- MatrixPlot + geom_point(data=d, col = "yellow", size = rel(BmSize)*1.4,
                                              shape=BestMatchesShape)

    # elemente mit und ohne klasse
    if(length(BestMatchesShape)==1){
      MatrixPlot <- MatrixPlot + geom_point(aes_string(y = 'y', x='x', col='factor(class)'), data=d , size = rel(BmSize),
                                            shape=BestMatchesShape)
      # UmatrixPlot <- UmatrixPlot + geom_point(aes_string(y = 'y', x='x', col='factor(class)'), data=d2 , size = rel(BmSize),
      #                                       shape=BestMatchesShape)
    }
    else{
      MatrixPlot <- MatrixPlot + geom_point(aes_string(y = 'y', x='x', col='factor(class)', shape='factor(class)'), data=d ,
                                              stroke=BmSize)#lwd=3)#size = rel(BmSize), lwd=3)
      # UmatrixPlot <- UmatrixPlot + geom_point(aes_string(y = 'y', x='x', col='factor(class)', shape='factor(class)'), data=d2,
      #                                         stroke=BmSize)#lwd=3)#size = rel(BmSize), lwd=3)
    }



    # add labels
    if(!is.null(BestMatchesLabels)){
      bestmatchLabels = data.frame(y = BestMatches[,2], x = BestMatches[,3], 'label' = BestMatchesLabels[as.numeric(rownames(BestMatches)),2])
      MatrixPlot <- MatrixPlot + geom_label(data=bestmatchLabels,
                                              aes_string(label="label"),
                                              color=BestMatchesLabelStyle$color,
                                              fontface=BestMatchesLabelStyle$fontface,
                                              fill=BestMatchesLabelStyle$fill ,
                                              alpha=BestMatchesLabelStyle$alpha ,
                                              angle=BestMatchesLabelStyle$angle ,
                                              size=BestMatchesLabelStyle$size ,
                                              nudge_x =BestMatchesLabelStyle$nudge_x,
                                              nudge_y =BestMatchesLabelStyle$nudge_y )
      #UmatrixPlot <- UmatrixPlot + geom_text(data=bestmatchLabels, aes(label=label))
    }

    # mark duplicates
    if(nrow(duplicatedBestMatches)>0){
      if(MarkDuplicatedBestMatches){
        duplicatedBestMatchesMarker = data.frame(y = duplicatedBestMatches[,2]+1, x = duplicatedBestMatches[,3])
        MatrixPlot <- MatrixPlot + geom_point(data = duplicatedBestMatchesMarker,
                                                shape=24,
                                                color="red",
                                                fill="red",
                                                size=4)
      }
    }

  }

  return(MatrixPlot + ggtitle(Title) + scale_size_area())  # return the plot
  ############
  # draw Umatrix with base functions
  ############
  #
  # else if(Fast){
  #   par(mar=c(0.001, 0.001, 0.001, 0.001))
  #
  #   image(z=t(Matrix),x=1:ncol(Matrix), y=1:nrow(Matrix),
  #         col = Colormap, ylim=c(nrow(Matrix),1), xaxt='n', yaxt='n', ann=FALSE)
  #   contour(z = t(Matrix),x=1:ncol(Matrix), y=1:nrow(Matrix), add=T,
  #           nlevels=35,  drawlabels = F, col=rgb(0,0,0,0.5))
  #
  #   # add the BestMatches
  #   if(!is.null(BestMatches)){
  #     if(is.null(Cls)) Cls <- rep(1,nrow(BestMatches))
  #     uniqueClasses <- sort(na.last=T,unique(Cls))
  #     for( i in 1:length(uniqueClasses)){
  #       classMembers <- BestMatches[Cls == uniqueClasses[i],]
  #
  #       if(is.vector(classMembers)) classMembers <- matrix(classMembers, ncol=3, byrow=T)
  #
  #       if(length(classMembers) > 0){
  #         points(classMembers[,3], classMembers[,2], col=ClsColors[i], pch=19)
  #       }
  #     }
  #
  #     if(!is.null(BestMatchesLabels))
  #       text(BestMatches[,3], BestMatches[,2], labels=BestMatchesLabels, cex= 1)
  #
  #   }
  # }
}