Infercnv runs successfully and generated plots but they are blank

On Linux, one of the available graphical backends, Cairo, has limitations in both the maximum size of the image, and the maximum size of a matrix that can be plot in R. To get around this issue, we can use the alternative graphical backend Xlib.

If you are logging in to a remote server, first do the following:

• ssh with the -X (X11 forwarding) or -Y option (trusted X11 forwarding)
• run echo $DISPLAY to find out what it is set to
• within R, run Sys.setenv("DISPLAY"="result_of_previous_echo_display:with_the_port")

Then for all cases, run:

• within R, run options(bitmapType="Xlib")
• run infercnv (the whole analysis or just the plotting function on a reloaded object)