ctheodoris

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Thank you for your question. Some of the cell types were consolidated to match other data sources we are using for ongoing work. For example, all B cell subtypes were consolidated into B cells.

This is not not clear in the paper
Could you please explain it here ?

@ctheodoris

This is not not clear in the paper
Could you please explain it here ?

Even though consolidating all B subtypes into B cells, I am still left with 84 subtypes,

I can see only 3 b types cB1, cB2 and cB3. from column 'cl295v11SubShort'

anndata.obs.cl295v11SubShort.unique()

{'cTNI15', 'cM05', 'cTNI22', 'cB2', 'cE05', 'cTNI08', 'cTNI19', 'cTNI11', 'cS11', 'cE02', 'cS05', 'cP3', 'cS04', 'cTNI06', 'cM10', 'cTNI12', 'cP1', 'cTNI10', 'cTNI05', 'cM06', 'cS07', 'cE09', 'cE04', 'cE06', 'cTNI24', 'cTNI14', 'cS26', 'cTNI26', 'cTNI02', 'cS23', 'cS15', 'cTNI18', 'cS17', 'cS08', 'cB3', 'cS14', 'cM09', 'cE07', 'cS30', 'cTNI20', 'cM04', 'cM03', 'cS19', 'cM02', 'cS31', 'cS28', 'cS27', 'cS03', 'cTNI17', 'cE01', 'cTNI13', 'cM01', 'cS20', 'cP2', 'cS29', 'cS13', 'cE11', 'cTNI16', 'cS09', 'cS25', 'cS10', 'cS02', 'cTNI25', 'cM08', 'cTNI04', 'cM07', 'cS16', 'cS21', 'cE08', 'cMA01', 'cTNI01', 'cE10', 'cTNI07', 'cTNI09', 'cS01', 'cS06', 'cE03', 'cTNI23', 'cS18', 'cS22', 'cS12', 'cB1', 'cS33', 'cS32', 'cTNI21', 'cS24', 'cTNI03'}

@ctheodoris

This is one example where cell types were consolidated. Other cell types were also consolidated. This discussion page is for discussions related to the code on this repository. If you have further questions regarding the biological analyses in the paper, please email. Thank you!

@ctheodoris

Can you please clarify this. I am still waiting for your reply on this
How did you come up with 47/53 classes
Because in the original dataset I can see all tumour patients have unique 87 cell sub types as mentioned above and below

cell_subtypes from public dataset
['cE01 (Stem/TA-like)',
'cE03 (Stem/TA-like prolif)',
'cTNI05 (CD4+ IL17+)',
'cTNI04 (CD4+ IL7R+CCL5+)',
'cE05 (Enterocyte 2)',
'cS17 (Pericyte)',
'cM02 (Macrophage-like)',
'cE04 (Enterocyte 1)',
'cE02 (Stem/TA-like/Immature Goblet)',
'cTNI09 (CD4+ Treg prolif)',
'cE08 (Goblet)',
'cM09 (mregDC)',
'cTNI22 (cTNI22)',
'cS13 (Endo venous-like)',
'cM01 (Monocyte)',
'cS27 (CXCL14+ CAF)',
'cTNI11 (CD8+GZMK+)',
'cE09 (Best4)',
'cTNI08 (CD4+ Treg)',
'cM04 (DC2)',
'cTNI24 (NK GZMK+)',
'cB1 (B IGD+IgM+)',
'cMA01 (Mast)',
'cP2 (Plasma IgG)',
'cTNI10 (CD8+ IL7R+)',
'cB2 (B GC-like)',
'cTNI20 (PLZF+ T)',
'cE11 (Enteroendocrine)',
'cS08 (Endo arterial-like)',
'cTNI02 (CD4+ IL7R+SELL+)',
'cTNI13 (CD8+ T IL17+)',
'cM05 (DC2 C1Q+)',
'cB3 (B CD40+ GC-like)',
'cS29 (MMP3+ CAF)',
'cS02 (Endo capillary)',
'cS12 (Endo)',
'cP1 (Plasma IgA)',
'cS15 (Pericyte)',
'cTNI25 (NK XCL1+)',
'cTNI18 (gd-like T PDCD1+)',
'cE06 (Immature Goblet)',
'cTNI17 (gd-like T)',
'cTNI16 (CD8+ CXCL13+ prolif)',
'cS18 (Pericyte)',
'cS04 (Endo)',
'cE10 (Tuft)',
'cTNI23 (NK CD16A+)',
'cM10 (Granulocyte)',
'cM06 (DC IL22RA2)',
'cS11 (Endo proif)',
'cS09 (Endo)',
'cTNI03 (CD4+ IL7R+HSP+)',
'cS19 (Pericyte)',
'cTNI06 (CD4+ TFH)',
'cTNI01 (CD4+ IL7R+)',
'cM03 (DC1)',
'cTNI07 (CD4+ CXCL13+)',
'cS25 (Fibro CCL8+)',
'cS28 (GREM1+ CAF)',
'cE07 (Goblet/Enterocyte)',
'cP3 (Plasma IgG prolif)',
'cS10 (Endo tip cells)',
'cTNI26 (ILC3)',
'cTNI14 (CD8+ CXCL13+)',
'cS32 (Smooth Muscle)',
'cTNI21 (PLZF+ T prolif)',
'cM07 (pDC)',
'cTNI12 (CD8+ IL7R+)',
'cS24 (Fibro BMP-producing)',
'cTNI15 (CD8+ CXCL13+ HSP+)',
'cS01 (Endo arterial)',
'cS30 (CAF CCL8 Fibro-like)',
'cM08 (AS-DC)',
'cS20 (Pericyte prolif)',
'cS14 (Endo)',
'cTNI19 (gd-like T prolif)',
'cS06 (Endo lymphatic)',
'cS16 (Pericyte)',
'cS26 (Myofibro)',
'cS31 (CAF stem niche Fibro-like)',
'cS22 (Fibro stem cell niche)',
'cS33 (Schwann)',
'cS05 (Endo venous)',
'cS03 (Endo capillary)',
'cS23 (Fibro BMP-producing)',
'cS21 (Fibro stem cell niche)',
'cS07 (Endo capillary-like)']

You clarified in one correspondance that you treated all Epithelial cells (=11 sub types) as malignant. How did you sub group others (46. This is really confusing). Even if you choose these epithelial cells as one class , the sum should be 46 + 11 not 53.
Or Did you group Epi cells as follows

Epi_sub_group 1: cE01 (Stem/TA-like)', 'cE03 (Stem/TA-like prolif)', 'cE02 (Stem/TA-like/Immature Goblet)'
Epi_sub_group 2: 'cE02 (Stem/TA-like/Immature Goblet)', 'cE08 (Goblet)', 'cE07 (Goblet/Enterocyte)', 'cE06 (Immature Goblet)',
Epi_sub_group 3: 'cE05 (Enterocyte 2)',
Epi_sub_group 4: 'cE04 (Enterocyte 1)',
Epi_sub_group 5: 'cE09 (Best4)',
Epi_sub_group 6 'cE11 (Enteroendocrine)',
Epi_sub_group 7: 'cE10 (Tuft)',

Can you please clarify this