Configuring trajectories with dc.tl.TConfig

azizilab / decipher

A single-cell analysis toolkit to jointly analyze samples from distinct conditions

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Configuring trajectories with dc.tl.TConfig #3

Open lu-r-lu opened 9 months ago

lu-r-lu commented 9 months ago

Hello

I am new to using this type of tools, and I definitely need some help with using dc.tl.trajectories(). Would it be possible to receive a more detailed explanation on how to configure the trajectories using these functions? Especially with the format of the variables to feed into the dc.tl.TConfig function. I've tried to replicate the format used in the tutorial but all I get is errors

Thank you in advance All the best L.

itamarb-cgen commented 9 months ago

Hi,

You may want to verify first that the issue is not with the package itself. Check that the example works fine in your environment. I also got errors from dc.tl.trajectories() and I'm not sure but I suspect it may be related to python package versions.
Note that Dr. Azizi will give a talk later today (8:30-9:15 Pacific Standard Time) at the MLSB meeting and all the talks will be broadcasted through Youtube. From the title "Probabilistic modeling of dynamics in the tumor microenvironment" it seems that she will describe this and/or related methods. Best regards, Itamar

lu-r-lu commented 9 months ago

Thanks for the reply I actually got something to work, but I am unsure about how to properly control the input to output sequence. So I assume it isn't really an issue with the package version, but rather with myself not fully understanding what goes in in order to get the desired output. Will tune in for the talk later if available on Youtube. Might be useful for my understanding

All the best, L.

itamarb-cgen commented 9 months ago

Something like the following worked for me, where the numbers are the clusters produced by decipher:

dc.tl.cell_clusters(adata1)
dc.pl.decipher(adata1, ["decipher_clusters"],wspace=0.8)

dc.tl.trajectories(
   adata1,
   dc.tl.TConfig("G1", '20', '2', field, "G1"),
   dc.tl.TConfig("G2", '9', '16', "field", "G2"),
)
fig=dc.pl.trajectories(adata1, color=field)
plt.show()

lu-r-lu commented 9 months ago

Thank you. Something similar worked for me, too. What I am still struggling with a bit is setting up trajectories a bit more purposely, but getting there.