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hamrhein / mouse_embryo

Graphviz graphs using edge data from String-db
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How to generate input files #2

Open MinjieHu opened 4 years ago

MinjieHu commented 4 years ago

Hi hamrhein,

Thanks for the awesome codes for the beautiful figures.

In order to generate the Blossom graph or TF networks, it looks like I need to generate some input files, like peng_bloom_adjacency_matrix.tsv, peng_bloom_cluster_size_table.txt or MouseLimbData.h5. Could you give some explanation or code about how to generate these input?

Thanks!

Minjie

hamrhein commented 4 years ago

Hi Minjie,

I added the URLs for direct download of those files to the instructions for local execution, just like the Docker and Singularity recipes. I also added a list of pre-requisites for local execution. Thank you for drawing my attention to this.

--Henry

MinjieHu commented 4 years ago

Hi Henry,

Thanks for the quick reply. The link is very helpful to look into the data. As I trying to apply this method to my own data, could you give me more help about how to generate these files. Based on the data, I guess:

  1. Is peng_bloom_cluster_size_table.txt the file indicating the cell number for each cluster?
  2. peng_bloom_adjacency_matrix.tsv is the matrix information of TF for each cluster. While I am still not sure about the values in this matrix and how to generate these values.
  3. Is the MouseLimbData.h5 the TF gene expression matrix for each individual cell?