Following clonotypes between samples

[ASNbioinf]

I have a similar problem to #40. I have T cells that I clustered. There are clones shared between samples that belong to the same patient. I used clonalCompare() to show the proportion of each clone within the specified samples. Is there a function that allows me to plot the frequency of each clone within the specified samples instead of proportion? I mean, I like this plot, but I want to put the frequency in the y-axis.

[Qile0317]

@ncborcherding I don't believe there is an option to do this yet but the change should be pretty trivial - I can whip up a PR for this.

[ncborcherding]

@Qile0317,

That would be awesome if you can include it in the work you are doing. I think having an option to plot frequency or proportion in clonalCompare() would be perfect and then users could use exportTable for either.

Nick

[Qile0317]

@ncborcherding Just to make sure - are the proportions strictly supposed to be (Frequency of all clones) / (number of clones)? Trying to figure out if my code is incorrect or (probably not) the entire function has been doing faulty computations this whole time.

[ASNbioinf]

Proportion = count of clone / total clones in sample

[ncborcherding]

@Qile0317 Proportion = frequency of individual clone / total number of sequences in a sample.

[ncborcherding]

Fix is up in the dev version, we will do some more testing and it will be in the main branch soon. I'm going to close this issue.