cell type cluster - Githubissues

guanjue / IDEAS_2018

Jointly characterizing epigenetic dynamics across multiple cell types

MIT License

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cell type cluster #10

Open ximbao opened 4 years ago

ximbao commented 4 years ago

Hello,

I ran IDEAS for 18 cell lines and 4 epigenomic marks - My question is related to the cell type segmentation. Specifically:

VISUALIZATION: The included plot.R is a R script that visualizes the segmentation results. In R environment, load this file by source("plot.R").

(B) Show cell type clustering and epigenetic states: showPop() Example: showPop("toy.data", indlist=1:10, inv=1:1000, repn=2) First argument is the inputfile name. Second argument list which (replicate of) cell types (their indices, starting from 1) should be shown, if not specified, all will be shown. Third argument list which positions (their indices, starting from 1) should be shown, if not specified, all will be shown. Fourth argument specifies number of replicates per cell type (only works if the number of replicates for each cell is the same); not needed if no replicates.
```
        This function will show a figure with three parts, top one is the cell type clustering figure using results in *.cluster file; 
        middle one is the epigenetic state using results in *.state file;
        and bottom one is the position class using results in *.state file.
```

I can't find this R script and unless I'm missing something I don't think I have the means to generate this cel type clustering.

Any feedback would be appreciated.

Thanks,

Felipe