pegasus subset samples for scatter plot

[Lai Ping Wong]

hi,

Many thanks for a useful pegasus scRNA bioinformatics tool available for public usage.

I am a beginner of pegasus, I wonder whether pegasus scatter plot allows user to select samples (channel) to plot instead of entire set? if yes, please kindly provide an example of the command to use.

I tried the below but AssertionError

subsamp={'s1', 's2', 's3', 's6'}

eg:pg.scatter(dat, attrs = ['Channel'],restrictions = subsamp, basic = 'umap')

your input is highly appreciated.

thanks,

Regards,
Lai Ping

Department of Molecular Biology
Massachusetts General Hospital
Simches Research Center,
R2200
185 Cambridge St.
Boston, MA 02114.

[Yiming Yang]

Hi Lai Ping,

Thank you for reaching out!

Due to the documentation of "scatter" function (https://pegasus.readthedocs.io/en/latest/api/pegasus.scatter.html), the format of "restrictions" parameter should follow "attr:val1,val2,..." format. Taking your example, say if the sample info of your data is stored in "data.obs['Channel']", then you should use

pg.scatter(data, attrs=['Channel'], restrictions="Channel:s1,s2,s4,s6", basis='umap')

You can decide whether to show all the rest points or not by setting "show_background" parameter to True or False. If True, all the rest points will be shown in a grey faded color as background; if False, they won't appear in the resulting plot.

Moreover, you can add more restrictions. E.g.

pg.scatter(data, attrs=['Channel'], restrictions=["Channel:s1,s2,s4,s6", "louvain_labels:1,2"])

will only show points from s1, s2, s4, s6 samples AND belonging to Louvain cluster 1 and 2.

pg.scatter(data, attrs=['louvain_labels', 'Channel'], restrictions=["Channel:s1,s2,s4,s6", "louvain_labels:~1"])

will show points from the 4 samples and not belonging to Louvain cluster 1, and give you two UMAP plots colored by louvain_labels and Channel attributes, respectively.

Hope it helps!

Sincerely,

Yiming

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