{"action":"created","issue":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/359","repository_url":"https://api.github.com/repos/fidelram/deepTools","labels_url":"https://api.github.com/repos/fidelram/deepTools/issues/359/labels{/name}","comments_url":"https://api.github.com/repos/fidelram/deepTools/issues/359/comments","events_url":"https://api.github.com/repos/fidelram/deepTools/issues/359/events","html_url":"https://github.com/fidelram/deepTools/issues/359","id":154644523,"number":359,"title":"--xxxThreshold for plotHeatmap?","user":{"login":"MWSchmid","id":8819325,"avatar_url":"https://avatars.githubusercontent.com/u/8819325?v=3","gravatar_id":"","url":"https://api.github.com/users/MWSchmid","html_url":"https://github.com/MWSchmid","followers_url":"https://api.github.com/users/MWSchmid/followers","following_url":"https://api.github.com/users/MWSchmid/following{/other_user}","gists_url":"https://api.github.com/users/MWSchmid/gists{/gist_id}","starred_url":"https://api.github.com/users/MWSchmid/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MWSchmid/subscriptions","organizations_url":"https://api.github.com/users/MWSchmid/orgs","repos_url":"https://api.github.com/users/MWSchmid/repos","events_url":"https://api.github.com/users/MWSchmid/events{/privacy}","received_events_url":"https://api.github.com/users/MWSchmid/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-05-13T06:45:09Z","updated_at":"2016-05-13T08:59:26Z","closed_at":null,"body":"I think that it would be nice to have the \"--minThreshold\" and \"--maxThreshold\" arguments in plotHeatmap as well. computeMatrix with multiple samples can take quite a long time and being able to set the thresholds only during plotting would help to find a senseful value quicker (to kick out abnormal regions).\r\n\r\nNote aside - I assume that the sorting in plotHeatmap uses all data/samples for a given region at once, but somehow it isn't entirely clear to me from the documentation whether this is true (the alternative would be that each sample is sorted separately - meaning that one line along the plot does not reflect one region, but many)."},"comment":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/comments/218988855","html_url":"https://github.com/fidelram/deepTools/issues/359#issuecomment-218988855","issue_url":"https://api.github.com/repos/fidelram/deepTools/issues/359","id":218988855,"user":{"login":"MWSchmid","id":8819325,"avatar_url":"https://avatars.githubusercontent.com/u/8819325?v=3","gravatar_id":"","url":"https://api.github.com/users/MWSchmid","html_url":"https://github.com/MWSchmid","followers_url":"https://api.github.com/users/MWSchmid/followers","following_url":"https://api.github.com/users/MWSchmid/following{/other_user}","gists_url":"https://api.github.com/users/MWSchmid/gists{/gist_id}","starred_url":"https://api.github.com/users/MWSchmid/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MWSchmid/subscriptions","organizations_url":"https://api.github.com/users/MWSchmid/orgs","repos_url":"https://api.github.com/users/MWSchmid/repos","events_url":"https://api.github.com/users/MWSchmid/events{/privacy}","received_events_url":"https://api.github.com/users/MWSchmid/received_events","type":"User","site_admin":false},"created_at":"2016-05-13T08:59:26Z","updated_at":"2016-05-13T08:59:26Z","body":"Hi Devon\r\n\r\nRight - but the range of the heatmap legend/values seems to be quite senseful anyway - even with extreme outliers (i.e. regions with very high coverage at few spots) - in contrast to the profile where the outliers cause quite massive peaks. --yMin and --yMax are an option as well, but removing them entirely would be nicer as the profile gets quickly uninformative if there several \"outlier-peaks\". \r\n\r\n-.- \r\n\r\nI guess that setting --averageTypeSummaryPlot to median instead of mean would solve the problem as well (as long as the coverage is high enough)...\r\n\r\n^^\r\n\r\nBest regards,\r\n\r\nMarc"}}