R Circlize "Detect some gaps are too large"

Question

I would like make a similar graph posted here using our data, however, I received this error message “Detect some gaps are too large”. Do you think because some values are very small as compare to others (e.g.; 1 versus 1812)?. I made a few changes to my data as in matrix 2 by adding a few zeros after a 1 or 2 and it works. Is there any way to work around with this range of data? I would like to plot this beautiful graph using my real data (matrix 1). Any help is much appreciated. ``` library(circlize) #matrix 1 #level0 <- c(1, 8, 39, 14, 2) #level1 <- c(1, 19, 153, 93, 1) #level2 <- c(2, 19, 274, 46, 13) #level3 <- c(0, 8, 152, 1812, 465) #level4 <- c(0, 2, 1, 164, 226) #matrix 2 #level0 <- c(100,8,39,14,200) #level1 <- c(100,190, 153,93,100) #level2 <- c(200,19,274,646,130) #level3 <- c(200,800,152,1812,465) #level4 <- c(200,200,100,164,226) #build matrix 2 a <- list(c(100,8,39,14,200),c(100,19, 153,93,100), c(200,19,274,646,13), c(200,8,152,1812,465),c(200,200,100,164,226)) mat <-…

Accepted Answer

So I think your `df1` object is a little different to my original code. If you set up the matrix `m` and `df1` as such... ``` m <- matrix(c(1, 8, 39, 14, 2, 1, 19, 153, 93, 1, 2, 19, 274, 46, 13, 0, 8, 152, 1812, 465, 0, 2, 1, 164, 226), nrow=5, byrow=TRUE) df1 <- data.frame(order=1:5, region=paste0("level",1:5), rcol = c("red", "orange", "yellow", "green", "blue"), lcol = c("#FF000020", "#FFA50020", "#FFFF0020", "#00FF0020", "#0000FF20"), stringsAsFactors=FALSE) df1$region <- factor(df1$region, levels=df1$region) df1$xmin <- 0 df1$xmax <- rowSums(m)+colSums(m) n <-nrow(df1) dimnames(m) <- list(orig=df1$region,dest=df1$region) ``` You get the following objects... ``` > df1 order region rcol lcol xmin xmax 1 1 level1 red #FF000020 0 68 2 2 level2 orange #FFA50020 0 323 3 3 level3 yellow #FFFF0020 0 973 4 4 level4 green #00FF0020 0 4566 5 5 level5 blue #0000FF20 0 1100 > addmargins(m) dest orig level1 level2 level3 level4 level5 Sum level1 1 8 39 14 2 64 level2 1 19 153 93 1 267 level3 2 19 274 46 13 354 level4 0 8 152 1812 465 2437 level5 0 2 1 164 226 393 Sum 4 56 619 2129 707 3515 ``` I explain in more detail the purpose of `df1` in the working paper. Briefly, the `df1` object contains information on the lengths of sectors to be plotted (`xmin` and `xmax`) and the colours for the circle rectangles on the outside `rcol` and ribbon link colours `lcol`. You could of course have the same `lcol` and `rcol`,...adapt away until you get a palette/style that you like (perhaps a little less transparency for the `lcol`). You can then go ahead and use very similar code as to what I have in the demo file in the migest package to get a plot (I only changed the `circos.axis` axis arguments and the subset of `df2`)... ``` library(circlize) library(plyr) par(mar=rep(0,4)) circos.clear() #basic circos graphic parameters circos.par(cell.padding=c(0,0,0,0), track.margin=c(0,0.15), start.degree = 90, gap.degree =4) #sector details circos.initialize(factors = df1$region, xlim = cbind(df1$xmin, df1$xmax)) #plot sectors circos.trackPlotRegion(ylim = c(0, 1), factors = df1$region, track.height=0.1, #panel.fun for each sector panel.fun = function(x, y) { #select details of current sector name = get.cell.meta.data("sector.index") i = get.cell.meta.data("sector.numeric.index") xlim = get.cell.meta.data("xlim") ylim = get.cell.meta.data("ylim") #plot labels circos.text(x=mean(xlim), y=2.2, labels=name, facing = "arc", cex=0.8) #plot main sector circos.rect(xleft=xlim[1], ybottom=ylim[1], xright=xlim[2], ytop=ylim[2], col = df1$rcol[i], border=df1$rcol[i]) #blank in part of main sector #circos.rect(xleft=xlim[1], ybottom=ylim[1], xright=xlim[2]-rowSums(m)[i], ytop=ylim[1]+0.3, col = "white", border = "white") #white line all the way around #circos.rect(xleft=xlim[1], ybottom=0.3, xright=xlim[2], ytop=0.32, col = "white", border = "white") #plot axis circos.axis(labels.cex=0.6, major.at=seq(from=0,to=floor(df1$xmax)[i],by=500), labels.away.percentage = 0.15) }) ## ##plot links ## #add sum values to df1, marking the x-position of the first links out (sum1) and in (sum2). Updated for further links in loop below. df1$sum1 <- colSums(m) df1$sum2 <- numeric(n) #create a data.frame of matrix sorted by element size, to allow largest plotted first df2 <- cbind(as.data.frame(m),orig=rownames(m), stringsAsFactors=FALSE) df2 <- reshape(df2, idvar="orig", varying=list(1:n), direction="long", timevar="dest", time=rownames(m), v.names = "m") df2 <- arrange(df2,desc(m)) #loose non zero links df2 <- subset(df2, m>0) #plot links for(k in 1:nrow(df2)){ #i,j reference of flow matrix i<-match(df2$orig[k],df1$region) j<-match(df2$dest[k],df1$region) #plot link circos.link(sector.index1=df1$region[i], point1=c(df1$sum1[i], df1$sum1[i] + abs(m[i, j])), sector.index2=df1$region[j], point2=c(df1$sum2[j], df1$sum2[j] + abs(m[i, j])), col = df1$lcol[i]) #update sum1 and sum2 for use when plotting the next link df1$sum1[i] = df1$sum1[i] + abs(m[i, j]) df1$sum2[j] = df1$sum2[j] + abs(m[i, j]) } ``` Which gives a plot like this... If you want to add some directionality to the plot then uncomment the two lines in `panel.fun` which add the white rectangles and boarder line.

R Circlize "Detect some gaps are too large"

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