Controlling margins in a genoPlotR plot_gene_map

I'm producing a plot_gene_map figure by the genoPlotR R package, which gives a horizontal phylogenetic tree where aligned with each leaf is a genomic segment.

Here's a simple example that illustrates my usage and problem:

The plot_gene_map function requires an ade4s' package phylog object which represents the phylogenetic tree:

tree <- ade4::newick2phylog("(((A:0.08,B:0.075):0.028,(C:0.06,D:0.06):0.05):0.0055,E:0.1);")

A list of genoPlotR's dna_seg objects (which are essentially data.frames with specific columns), where the names of the list elements have to match the names of the leaves of tree:

dna.segs.list <- list(A=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.A.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="red")),
                      B=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.B.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="blue")),
                      C=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.C.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="green")),
                      D=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.D.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="yellow")),
                      E=genoPlotR::as.dna_seg(data.frame(name=paste0("VERY.LONG.NAME.E.",1:10),start=seq(1,91,10),end=seq(5,95,10),strand=1,col="black",ly=1,lwd=1,pch=1,cex=1,gene_type="blocks",fill="orange")))

And a list of genoPlotR's annotation objects, which give coordinate information, also named according to the tree leaves:

annotation.list <- lapply(1:5,function(s){
  mids <- genoPlotR::middle(dna.segs.list[[s]])
  return(genoPlotR::annotation(x1=mids,x2=NA,text=dna.segs.list[[s]]$name,rot=30,col="black"))
})
names(annotation.list) <- names(dna.segs.list)

And the call to the function is:

genoPlotR::plot_gene_map(dna_segs=dna.segs.list,tree=tree,tree_width=2,annotations=annotation.list,annotation_height=1.3,annotation_cex=0.9,scale=F,dna_seg_scale=F)

Which gives:

As you can see the top and right box (gene) names get cut off.

I tried playing with pdf's width and height, when saving the figure to a file, and with the margins through par's mar, but they have no effect.

Any idea how to display this plot without getting the names cut off?
Currently genoPlotR's plot_gene_map does not have a legend option implemented. Any idea how can I add a legend, let's say which shows these colors in squares aside these labels:

data.frame(label = c("A","B","C","D","E"), color = c("red","blue","green","yellow","orange"))

Glad that you like genoPlotR.

There are no real elegant solution to your problem, but here are a few things you can attempt: - increase annotation_height and reduce annotation_cex - increase rotation (“rot”) in the annotation function - use xlims to artificially increase the length of the dna_seg (but that’s a bad hack)

For the rest (including the legend), you’ll have to use grid and its viewports.

A blend of the first 3 solutions:

annotation.list <- lapply(1:5,function(s){
  mids <- genoPlotR::middle(dna.segs.list[[s]])
  return(genoPlotR::annotation(x1=mids, x2=NA, text=dna.segs.list[[s]]$name,rot=75,col="black"))
})
names(annotation.list) <- names(dna.segs.list)
genoPlotR::plot_gene_map(dna_segs=dna.segs.list,tree=tree,tree_width=2,annotations=annotation.list,annotation_height=5,annotation_cex=0.4,scale=F,dna_seg_scale=F, xlims=rep(list(c(0,110)),5))

For the better solution with grid: (note the "plot_new=FALSE" in the call to plot_gene_map)

# changing rot to 30
annotation.list <- lapply(1:5,function(s){
 mids <- genoPlotR::middle(dna.segs.list[[s]])
return(genoPlotR::annotation(x1=mids,x2=NA,text=dna.segs.list[[s]]$name,rot=30,col="black"))
})
names(annotation.list) <- names(dna.segs.list)


# main viewport: two columns, relative widths 1 and 0.3
pushViewport(viewport(layout=grid.layout(1,2, widths=unit(c(1, 0.3), rep("null", 2))), name="overall_vp"))
# viewport with gene_map
pushViewport(viewport(layout.pos.col=1, name="geneMap"))
genoPlotR::plot_gene_map(dna_segs=dna.segs.list,tree=tree,tree_width=2,annotations=annotation.list,annotation_height=3,annotation_cex=0.5,scale=F,dna_seg_scale=F, plot_new=FALSE)
upViewport()
# another viewport for the margin/legend
pushViewport(viewport(layout.pos.col=2, name="legend"))
plotLegend(…)
upViewport()

Hope that helps!

Lionel