{"action":"created","issue":{"url":"https://api.github.com/repos/KenLauLab/pCreode/issues/2","repository_url":"https://api.github.com/repos/KenLauLab/pCreode","labels_url":"https://api.github.com/repos/KenLauLab/pCreode/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/KenLauLab/pCreode/issues/2/comments","events_url":"https://api.github.com/repos/KenLauLab/pCreode/issues/2/events","html_url":"https://github.com/KenLauLab/pCreode/issues/2","id":293165950,"number":2,"title":"Qualitative MetaData as Overlay for the graph?","user":{"login":"charles-bernard","id":23334620,"avatar_url":"https://avatars3.githubusercontent.com/u/23334620?v=4","gravatar_id":"","url":"https://api.github.com/users/charles-bernard","html_url":"https://github.com/charles-bernard","followers_url":"https://api.github.com/users/charles-bernard/followers","following_url":"https://api.github.com/users/charles-bernard/following{/other_user}","gists_url":"https://api.github.com/users/charles-bernard/gists{/gist_id}","starred_url":"https://api.github.com/users/charles-bernard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/charles-bernard/subscriptions","organizations_url":"https://api.github.com/users/charles-bernard/orgs","repos_url":"https://api.github.com/users/charles-bernard/repos","events_url":"https://api.github.com/users/charles-bernard/events{/privacy}","received_events_url":"https://api.github.com/users/charles-bernard/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-01-31T13:54:25Z","updated_at":"2018-02-02T14:59:08Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI was trying your tool today and I worked along with your tutorial without any problem but I had just one question or rather recommendation concerning the graph plot. If I manage to plot the level of expression of my genes of interest along the tree, I was wandering whether you also plan to enable to choose qualitative metadata as overlay for the graph plot?\r\n\r\nI understand that several cells can be projected on a node of the tree, so with a quantitative variable (i.e gene expression), it becomes easy to average this variable for all cells of each node, but there are also ways to deal with this with qualitative data.\r\n\r\nFor instance, you could treat each node as a pie chart or, even simpler, consider only the \"majority\" value among all the cells composing a node...  \r\n\r\nIf I'm asking that, it is because I'm trying to do pseudo time analysis and I would like to check how well the ordering of the cells in my p-creode tree matches the labels of my cells. \r\n\r\nThat would be great if such options could be implemented\r\n\r\nAll the best,\r\n\r\nCharles\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/KenLauLab/pCreode/issues/comments/362609157","html_url":"https://github.com/KenLauLab/pCreode/issues/2#issuecomment-362609157","issue_url":"https://api.github.com/repos/KenLauLab/pCreode/issues/2","id":362609157,"user":{"login":"charles-bernard","id":23334620,"avatar_url":"https://avatars3.githubusercontent.com/u/23334620?v=4","gravatar_id":"","url":"https://api.github.com/users/charles-bernard","html_url":"https://github.com/charles-bernard","followers_url":"https://api.github.com/users/charles-bernard/followers","following_url":"https://api.github.com/users/charles-bernard/following{/other_user}","gists_url":"https://api.github.com/users/charles-bernard/gists{/gist_id}","starred_url":"https://api.github.com/users/charles-bernard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/charles-bernard/subscriptions","organizations_url":"https://api.github.com/users/charles-bernard/orgs","repos_url":"https://api.github.com/users/charles-bernard/repos","events_url":"https://api.github.com/users/charles-bernard/events{/privacy}","received_events_url":"https://api.github.com/users/charles-bernard/received_events","type":"User","site_admin":false},"created_at":"2018-02-02T14:59:08Z","updated_at":"2018-02-02T14:59:08Z","author_association":"NONE","body":"Sorry I apologize, there is no mistake. In fact, I obtained something understandable with qualitative data turned into quantitative tab thanks to this parameter : upper_range... which I guess is relative to the values of the variable being plotted and not to the values of all the variables pooled together... In my case, with the node color being set to the most represented clusterID, I lose important information. \r\n\r\nSince igraph in python does not enable pie chart, I was wandering whether it is possible or not to choose myself the number of nodes used for the generation of the graphs (like in Spade for instance) ?\r\n\r\nThe rational behind this question is the following: the more nodes, the more likely one node = one cluster and not a mixture of clusters\r\n\r\n"}}
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