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skeleton for LR encoding ED model with extension of estimator #44

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merged 22 commits into from
Nov 7, 2021
Merged

skeleton for LR encoding ED model with extension of estimator #44

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f99ff95
skeleton for LR encoding ED model with extension of estimator
davidsebfischer Oct 12, 2021
f84f8a7
enabled extraction of scaled adj matrix
davidsebfischer Oct 12, 2021
162ba4e
debugged unit tests
davidsebfischer Oct 13, 2021
37ec983
added disclaimer
davidsebfischer Oct 13, 2021
64ae03e
Merge branch 'feature/lr_encoder' of github.com:theislab/ncem into fe…
AnnaChristina Oct 14, 2021
3dc14a3
simplify output layers with get_out in remaining models
AnnaChristina Oct 14, 2021
427ffb5
simplify output layers with get_out in remaining models
AnnaChristina Oct 14, 2021
833ec07
add disclaimer to cond layers
AnnaChristina Oct 14, 2021
21f54c9
fix max and gcn layer for single gnn
AnnaChristina Oct 19, 2021
998c8cc
Bump version from 0.3.2 to 0.4.0
AnnaChristina Oct 25, 2021
01438aa
added node embedding and output weight saving in EDncem models
davidsebfischer Oct 28, 2021
7405baa
Merge pull request #53 from theislab/development
AnnaChristina Nov 3, 2021
e26132a
fix conflicts
AnnaChristina Nov 3, 2021
9209a78
Merge branch 'release' of github.com:theislab/ncem into release
AnnaChristina Nov 3, 2021
e61d30c
Merge pull request #54 from theislab/release
AnnaChristina Nov 3, 2021
0c2839e
Bump version from 0.4.6 to 0.4.7
AnnaChristina Nov 3, 2021
0e2711f
add n_top_genes to dataloader
AnnaChristina Nov 4, 2021
2f03c77
Bump version from 0.4.7 to 0.4.8
AnnaChristina Nov 4, 2021
be89c0b
add hgnc names for schuerch
AnnaChristina Nov 7, 2021
803063d
Merge branch 'feature/embedding_saving' of github.com:theislab/ncem i…
AnnaChristina Nov 7, 2021
8a4bcfa
add saving of LR names to model class
AnnaChristina Nov 7, 2021
bd2f900
Merge pull request #51 from theislab/feature/embedding_saving
AnnaChristina Nov 7, 2021
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add hgnc names for schuerch
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@AnnaChristina
AnnaChristina committed Nov 7, 2021
commit be89c0b9d7f0d0ea02d6436693cb44a9abbf9880
65 changes: 62 additions & 3 deletions ncem/data.py
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Expand Up @@ -15,7 +15,7 @@
from matplotlib.ticker import FormatStrFormatter
from matplotlib.tri import Triangulation
from omnipath.interactions import import_intercell_network
from pandas import read_csv, read_excel
from pandas import read_csv, read_excel, DataFrame
from scipy import sparse, stats
from tqdm import tqdm

Expand Down Expand Up @@ -2464,8 +2464,67 @@ def _register_celldata(self, n_top_genes: Optional[int] = None):
"CD57 - NK cells:Cyc_17_ch_4",
"MMP12 - matrix metalloproteinase:Cyc_21_ch_4",
]

celldata = AnnData(X=celldata_df[feature_cols], obs=celldata_df[["File Name", "patients", "ClusterName"]])
feature_cols_hgnc_names = [
'CD44',
'FOXP3',
'CD8A',
'TP53',
'GATA3',
'PTPRC',
'TBX21',
'CTNNB1',
'HLA-DR',
'CD274',
'MKI67',
'PTPRC',
'CD4',
'CR2',
'MUC1',
'TNFRSF8',
'CD2',
'VIM',
'MS4A1',
'LAG3',
'ATP1A1',
'CD5',
'IDO1',
'KRT1',
'ITGAM',
'NCAM1',
'ACTA1',
'BCL2',
'IL2RA',
'ITGAX',
'PDCD1',
'GZMB',
'EGFR',
'VISTA',
'FUT4',
'ICOS',
'SYP',
'GFAP',
'CD7',
'CD247',
'CHGA',
'CD163',
'PTPRC',
'CD68',
'PECAM1',
'PDPN',
'CD34',
'CD38',
'SDC1',
'HOECHST1:Cyc_1_ch_1', ##
'CDX2',
'COL6A1',
'CCR4',
'MMP9',
'TFRC',
'B3GAT1',
'MMP12'
]
X = DataFrame(np.array(celldata_df[feature_cols]), columns=feature_cols_hgnc_names)
celldata = AnnData(X=X, obs=celldata_df[["File Name", "patients", "ClusterName"]])

celldata.uns["metadata"] = metadata
img_keys = list(np.unique(celldata_df[metadata["image_col"]]))
Expand Down