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ManuSetty / wishbone

Wishbone is an algorithm to align cells along developmental trajectories with branches
GNU General Public License v2.0
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Color cells by phenotype information. #49

Closed anushishah closed 7 years ago

anushishah commented 7 years ago

Hi Manu,

Is there a way to color the cells in the branches/trunk by phenotype information? E.g if I want to overlay color cells by samples names.

Thanks.

ManuSetty commented 7 years ago

I am not sure I understand. What kind of plot are you thinking about?

anushishah commented 7 years ago

wishbone_plot

I have attached a picture of the plot I am thinking of. Something where the user can give prior information of each cell like sample name, cell type, state, treatment, etc. So the plot can overlay such information.

Please let me know if it makes sense. And also please don't worry if it's too complicated or not really useful feature for wishbone.

ManuSetty commented 7 years ago

You can look at the Clustering of cells section for plots similar to this. The sample type can be used instead of clusters by setting scdata.cluster_assignments to the sample types. Then you can use plot_phenograph_clusters to make the plot required.