Plotting by chromosome

[cjy8709]

Hi! TWISST is great and I haven't had any problems so far, but I was wondering if you had a suggestion on how to plot the TWISST result by chromosome? Mostly how to plot it so that each chromosome would be on the same scale? If you have topology weight across the chromosomes seems like the plotting results are shown for all regions?

[simonhmartin]

Hi, I'm not sure exactly what you're asking. Check out my latest updates to the plot_twisst.R script. This now automatically separates chromosomes with different names when importing the data, even if thy're in a single file.
Using the plot.twisst function you have an option to concatenate chromosomes (with a specified gap) or to plot them separately, in which case you can use the ncol_weights option to to specify the number of columns of chromosomes to plot.
I think the best way to get the scales right is to set the xlim so that the maximum is the length of your longest chromosome. I just discovered that this option wasn't working in the plot.twisst function, but I have just pushed up a fix.
Does this help?

[simonhmartin]

Just to add, I have now added an option to subset the Twisst object by chromosomes, which can be used like this:

regions <- c("contig0")

twisst_data_contig0 <- subset.twisst.by.regions(twisst_data, regions)