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sidhomj / DeepTCR

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
https://sidhomj.github.io/DeepTCR/
MIT License
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No Sample Labels on Dendrogramplots #55

Closed jkbenotmane closed 2 years ago

jkbenotmane commented 2 years ago

Hello Prof. Sidhom, thank you for creating DeepTCR, it is a very useful & cool tool.

The Issue I experience when creating the Dendrogramplots is that the Circles of the Samples are getting labeled (by Sample/Class) in very unreadable colors, almost undistinguishable from the background.

Code

DTCRU.Repertoire_Dendrogram(n_jobs=40,distance_metric='correlation',sample_labels=True)
DTCRU.Repertoire_Dendrogram(n_jobs=40,distance_metric='correlation',log_scale=True,Load_Prev_Data=True,sample_labels=True)

Output

UMAP transformation...
PhenoGraph Clustering...
Finding 30 nearest neighbors using minkowski metric and 'auto' algorithm
Neighbors computed in 5.6398985385894775 seconds
Jaccard graph constructed in 1.4102559089660645 seconds
Wrote graph to binary file in 0.9278509616851807 seconds
Running Louvain modularity optimization
After 1 runs, maximum modularity is Q = 0.970462
Louvain completed 21 runs in 2.248636484146118 seconds
PhenoGraph complete in 10.259825944900513 seconds
Clustering Done
/home/patrick/anaconda3/envs/DEEPTCR_ENV/lib/python3.8/site-packages/DeepTCR/functions/utils_u.py:161: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. In future versions, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = copy.copy(mpl.cm.get_cmap("viridis"))
  cmap_viridis.set_under(color='white', alpha=0)
/home/patrick/anaconda3/envs/DEEPTCR_ENV/lib/python3.8/site-packages/DeepTCR/functions/utils_u.py:161: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. In future versions, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = copy.copy(mpl.cm.get_cmap("viridis"))
  cmap_viridis.set_under(color='white', alpha=0)

SPTCR_Dendrogram_correlation SPTCR_Dendrogram_correlation_log

Is it possible to change the font color of every Sample Labels ?