Thank you for a great tool and all the support I have received so far. I am now finalising my figures for a manuscript and I have some issues with the readability of the variables in the circosplots, i.e. at 6 o’clock and 12 o’clock when they are flipped, they overlap as you can see in the attached example. How can I make them all centrally align to their coloured bos as they do at around 3 and 9 o’clock?
I very much appreciate your help!
@aljabadi @kimanh.lecao I know you are very busy but I hope you can help me with this in order to finalise the figures for our manuscript
Thank you so much!
@aljabadi @kimanh.lecao We are very close to submission right now. Could you please help? Some of the plots have even more overlap at 6 and. 12 o’clock than the one in the example making it impossible to read those labels.
We dont have much time to respond to all the questions on this forum!
There is no quick fix we can provide at this stage. One would be to play with the arguments
size.variables. It will not be a deal breaker for a first submission of the manuscript! The other option is to extract the similarity matrix:
output = circosPlot(nutrimouse.sgccda, cutoff = 0.7, size.legend = 1.1)
And then you can use cytoscape or any other software to represent this signature as networks style.
I suggested @stepra to run the code below, and the figures looked much better.
pdf(file = "My_Circosplot_Plot.pdf", width = 7.3, height = 7.3) circosPlot(MY_DIABLO_OBJECT, cutoff = 0.7, line = F, comp = c(1,2), color.blocks= c('yellow', 'grey'), color.cor = c("pink","purple"), size.variables = 0.5, block.labels.adj = -1, var.adj = -0.7) dev.off()
Exporting the figure as a PDF with similar height and width has always produced the best results for me.
Yes, it worked like a charm! I had to increase the size of the pdf to accommodate the longest variable names to 8 only. But I very much appreciate your help @christoa. The manuscript is submitted