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ChenWeiyan / LandSCENT

Landscape Single Cell Entropy
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Plot_DiffusionMap colour by phenotype #15

Closed KatharinaKohler closed 3 years ago

KatharinaKohler commented 3 years ago

Hi Weiyan,

Thank you so much for previous help! Now the whole thing is working for me. I was just wondering whether there is the possibility to colour the dots according to phenotype information when doing the DiffusionMap? I haven't found any solution so far.

Best regards, Katharina

ChenWeiyan commented 3 years ago

Hi Katharina,

Using the Plot_DiffusionMap function itself is difficult to color the dots by phenotype. But you can simply extract the DiffusionMap's coordinates from the final object after the DiffusionMap is done, with the following command:

DM.coordinates <- DoDiffusionMap.o$DMEigen

And you will find the coordinates in columns. Furthermore, if you want the DPT information, you can try the following:

DPT <- destiny::DPT(DoDiffusionMap.o$DM, tips = DoDiffusionMap.o$root)

Once you get the DiffusionMap's coordinates and so on, you can then plot the figure you need with general tools, say ggplot2 etc.

Hope this be helpful, Weiyan

KatharinaKohler commented 3 years ago

This is very helpful, thank you so much!

Best regards, Katharina