Manipulating axis titles in ggpairs (GGally)
Short answer: There doesn't seem to be an elegant or easy way to do it, but here's a workaround.
I dug into the ggpairs source code (in the GGally package source available from CRAN) to see how the variable labels are actually drawn. The relevant function in ggpairs.R is print.ggpairs. It turns out the variable labels aren't part of the ggplot objects in each cell of the plot matrix -- i.e. they're not axis titles, which is why they aren't affected by using theme(axis.title.x = element_text(angle = 45) or similar.
Rather, they seem to be drawn as text annotations using grid.text (in package 'grid'). grid.text takes arguments including x, y, hjust, vjust, rot (where rot is angle of rotation), as well as font size, font family, etc. using gpar (see ?grid.text), but it looks like there is currently no way to pass in different values of those parameters to print.ggpairs -- they're fixed at default values.
You can work around it by leaving your variable labels blank to begin with, and then adding them on later with customized placement, rotation, and styling, using a modification of the relevant part of the print.ggpairs code. I came up with the following modification. (Incidentally, because the original GGally source code was released under a GPL-3 license, so is this modification.)
customize.labels <- function( plotObj, varLabels = NULL, #vector of variable labels titleLabel = NULL, #string for title leftWidthProportion = 0.2, #if you changed these from default... bottomHeightProportion = 0.1, #when calling print(plotObj),... spacingProportion = 0.03, #then change them the same way here so labels will line up with plot matrix. left.opts = NULL, #see pattern in left.opts.default bottom.opts = NULL, #see pattern in bottom.opts.default title.opts = NULL) { #see pattern in title.opts.default require('grid') vplayout <- function(x, y) { viewport(layout.pos.row = x, layout.pos.col = y) } numCol <- length(plotObj$columns) if (is.null(varLabels)) { varLabels <- colnames(plotObj$data) #default to using the column names of the data } else if (length(varLabels) != numCol){ stop('Length of varLabels must be equal to the number of columns') } #set defaults for left margin label style left.opts.default <- list(x=0, y=0.5, rot=90, just=c('centre', 'centre'), #first gives horizontal justification, second gives vertical gp=list(fontsize=get.gpar('fontsize'))) #set defaults for bottom margin label style bottom.opts.default <- list(x=0, y=0.5, rot=0, just=c('centre', 'centre'),#first gives horizontal justification, second gives vertical gp=list(fontsize=get.gpar('fontsize'))) #set defaults for title text style title.opts.default <- list(x = 0.5, y = 1, just = c(.5,1), gp=list(fontsize=15)) #if opts not provided, go with defaults if (is.null(left.opts)) { left.opts <- left.opts.default } else{ not.given <- names(left.opts.default)[!names(left.opts.default) %in% names(left.opts)]if (length(not.given)>0){ left.opts[not.given] <- left.opts.default[not.given]} }if (is.null(bottom.opts)) { bottom.opts <- bottom.opts.default} else{ not.given <- names(bottom.opts.default)[!names(bottom.opts.default) %in% names(bottom.opts)]if (length(not.given)>0){ bottom.opts[not.given] <- bottom.opts.default[not.given]}}if (is.null(title.opts)) { title.opts <- title.opts.default} else{ not.given <- names(title.opts.default)[!names(title.opts.default) %in% names(title.opts)]if (length(not.given)>0){ title.opts[not.given] <- title.opts.default[not.given]}} showLabels <- TRUE viewPortWidths <- c(leftWidthProportion, 1, rep(c(spacingProportion,1), numCol - 1)) viewPortHeights <- c(rep(c(1, spacingProportion), numCol - 1), 1, bottomHeightProportion)viewPortCount <- length(viewPortWidths)if(!is.null(titleLabel)){ pushViewport(viewport(height = unit(1,"npc") - unit(.4,"lines"))) do.call('grid.text', c(title.opts[names(title.opts)!='gp'], list(label=titleLabel, gp=do.call('gpar', title.opts[['gp']])))) popViewport()} # viewport for Left Names pushViewport(viewport(width=unit(1, "npc") - unit(2,"lines"), height=unit(1, "npc") - unit(3, "lines"))) ## new for axis spacingProportion pushViewport(viewport(layout = grid.layout( viewPortCount, viewPortCount, widths = viewPortWidths, heights = viewPortHeights ))) # Left Side for(i in 1:numCol){ do.call('grid.text', c(left.opts[names(left.opts)!='gp'], list(label=varLabels[i], vp = vplayout(as.numeric(i) * 2 - 1 ,1), gp=do.call('gpar', left.opts[['gp']])))) } popViewport()# layout popViewport()# spacing # viewport for Bottom Names pushViewport(viewport(width=unit(1, "npc") - unit(3,"lines"), height=unit(1, "npc") - unit(2, "lines"))) ## new for axis spacing pushViewport(viewport(layout = grid.layout( viewPortCount, viewPortCount, widths = viewPortWidths, heights = viewPortHeights))) # Bottom Side for(i in 1:numCol){ do.call('grid.text', c(bottom.opts[names(bottom.opts)!='gp'], list(label=varLabels[i], vp = vplayout(2*numCol, 2*i), gp=do.call('gpar', bottom.opts[['gp']])))) } popViewport() #layout popViewport() #spacing}And here's an example of calling that function:
require('data.table')require('GGally')require('grid')fake.data <- data.table(test.1=rnorm(50), #make some fake data for demonstration test.2=rnorm(50), test.3=rnorm(50), test.4=rnorm(50))g <- ggpairs(data=fake.data, columnLabels=rep('', ncol(fake.data)))#Set columnLabels to a vector of blank column labels#so that original variable labels will be blank.print(g)customize.labels(plotObj=g, titleLabel = 'Test plot', #string for title left.opts = list(x=-0.5, #moves farther to the left, away from vertical axis y=0.5, #centered with respect to vertical axis just=c('center', 'center'), rot=90, gp=list(col='red', fontface='italic', fontsize=12)), bottom.opts = list(x=0.5, y=0, rot=45, #angle the text at 45 degrees just=c('center', 'top'), gp=list(col='red', fontface='bold', fontsize=10)), title.opts = list(gp=list(col='green', fontface='bold.italic')))(This makes some very ugly labels -- for the purposes of demonstration only!)
I didn't tinker with placing the labels somewhere other than the left and bottom -- as in your Geovisualist example -- but I think you'd do it by changing the arguments to vplayout in the "Left Side" and "Bottom Side" pieces of code in customize.labels. The x and y coordinates in grid.text are defined relative to a viewport, which divides the display area into a grid in
pushViewport(viewport(layout = grid.layout( viewPortCount, viewPortCount, widths = viewPortWidths, heights = viewPortHeights )))The call to vplayout specifies which cell of the grid is being used to position each label.
Caveat: not a complete answer but perhaps suggests a way to approach it. You can do this by editing the grid objects.
# Plot in current window# use left to add space at y axis and bottom for below xaxis# see ?print.ggpairsprint(pairs.chrt, left = 1, bottom = 1)# Get list of grobs in current window and extract the axis labels# note if you add a title this will add another text grob, # so you will need to tweak this so not to extract itg <- grid.ls(print=FALSE)idx <- g$name[grep("text", g$name)]# Rotate yaxis labels# change the rot value to the angle you wantfor(i in idx[1:6]) { grid.edit(gPath(i), rot=0, hjust=0.25, gp = gpar(col="red")) }# Remove extra ones if you wantn <- ncol(airquality)lapply(idx[c(1, 2*n)], grid.remove)
My answer won't fix the diagonal label issue but it will fix the overlay one.
I had this issue with the report I am currently writing, where the axis titles were always over the axes, especially in ggpairs. I used a combination of adjusting the out.height/out.width in conjunction with fig.height/fig.width. Separately the problem was not fixed, but together it was. fig.height/fig.width took the labels away from the axis but made them too small to read, and out.height/out.width just made the plot bigger with the problem unchanged. The below gave me the results shown:
out.height="400px", out.width="400px",fig.height=10,fig.width=10before:plot with issues
after:
