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asntech / intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
http://intervene.rtfd.io/
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pairwise function have problems on --names and --sort #15

Closed clouds-drift closed 5 years ago

clouds-drift commented 5 years ago

Sorry, the --names is fine. But, it automatically sort the label by name and I can't change the label order. I'm using intervene version 0.6.4

cmd=paste("intervene pairwise -i", peak.file, "--output ../graph/Peak_without_control --filenames --compute frac --htype color --figsize 10 10 --project marker_pairwise_heatmap --diagonal", --names my.name, sep=""))

asntech commented 5 years ago

I have noticed that you have --filenames and then also using the --names. Can you try by the --filenames. Once --filenames is set then it ignores the --names.

clouds-drift commented 5 years ago

I have noticed that you have --filenames and then also using the --names. Can you try by the --filenames. Once --filenames is set then it ignores the --names. Yes, that's true and the --names and --filenames work well . I'm sorry for my title make some misunderstanding. But the --sort switch seems not working. Whatever --sort is, it always sort the provided names.

Thanks.

asntech commented 5 years ago

--sort just sorts the bed regions not the provided labels or filename. But, I will test it and check what is wrong. You only need to set the --sort if you compute jaccard or reldist. In your example, you don't the --sort since you're computing the fraction of overlap.

clouds-drift commented 5 years ago

Thank you for the explanation! I'm sorry for the misunderstanding of "--sort". So it seems there's no parameter to switch off the order of label name. It automatically order the provided label names.