Please check if appropriate organism/ID type was provided! Allowed proportion (0.98) of missing resource elements exceeded (1.00).
Closed this issue ยท 10 comments
When running this, I get the error above:
cellphonedb(adata, groupby='cluster_labels', expr_prop=0.1, resource_name='mouseconsensus', verbose=True, key_added='cpdb_res')
My adata contains the gene names, the normalised SCT assay (layer = data) as required, and the barcodes.
My dataset is mouse data and so here, I'm using the mouse consensus.
Another question, what if I want to run it through connectome, which value for the "key_added" parameter should I use?
Thanks in advance.
To be more specific, this is the error I got
@dbdimitrov
--------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[44], line 2
1 # run cellphonedb
----> 2 cellphonedb(adata, groupby='cluster_labels', expr_prop=0.1, resource_name='mouseconsensus', verbose=True, key_added='cpdb_res')
File [/data/leuven/345/vsc34524/miniconda3/envs/liana/lib/python3.10/site-packages/liana/method/sc/_Method.py:250](https://ondemand.hpc.kuleuven.be/data/leuven/345/vsc34524/miniconda3/envs/liana/lib/python3.10/site-packages/liana/method/sc/_Method.py#line=249), in Method.__call__(self, adata, groupby, resource_name, expr_prop, min_cells, groupby_pairs, base, supp_columns, return_all_lrs, key_added, use_raw, layer, de_method, n_perms, seed, n_jobs, resource, interactions, mdata_kwargs, inplace, verbose)
247 else:
248 ad = adata
--> 250 liana_res = liana_pipe(adata=ad,
251 groupby=groupby,
252 resource_name=resource_name,
253 resource=resource,
254 interactions=interactions,
255 expr_prop=expr_prop,
256 min_cells=min_cells,
257 supp_columns=supp_columns,
258 return_all_lrs=return_all_lrs,
259 groupby_pairs=groupby_pairs,
260 base=base,
261 de_method=de_method,
262 verbose=verbose,
263 _score=self._method,
264 n_perms=n_perms,
265 seed=seed,
266 n_jobs=n_jobs,
267 use_raw=use_raw,
268 layer=layer,
269 )
270 if inplace:
271 adata.uns[key_added] = liana_res
File [/data/leuven/345/vsc34524/miniconda3/envs/liana/lib/python3.10/site-packages/liana/method/sc/_liana_pipe.py:143](https://ondemand.hpc.kuleuven.be/data/leuven/345/vsc34524/miniconda3/envs/liana/lib/python3.10/site-packages/liana/method/sc/_liana_pipe.py#line=142), in liana_pipe(adata, groupby, resource_name, resource, interactions, groupby_pairs, expr_prop, min_cells, base, de_method, n_perms, seed, verbose, use_raw, n_jobs, layer, supp_columns, return_all_lrs, _score, _methods, _consensus_opts, _aggregate_method)
140 resource = explode_complexes(resource)
142 # Check overlap between resource and adata
--> 143 assert_covered(np.union1d(np.unique(resource[P.ligand]),
144 np.unique(resource[P.receptor])),
145 adata.var_names, verbose=verbose)
147 # Filter Resource
148 resource = filter_resource(resource, adata.var_names)
File [/data/leuven/345/vsc34524/miniconda3/envs/liana/lib/python3.10/site-packages/liana/method/_pipe_utils/_pre.py:60](https://ondemand.hpc.kuleuven.be/data/leuven/345/vsc34524/miniconda3/envs/liana/lib/python3.10/site-packages/liana/method/_pipe_utils/_pre.py#line=59), in assert_covered(subset, superset, subset_name, superset_name, prop_missing_allowed, verbose)
53 if prop_missing > prop_missing_allowed:
54 msg = (
55 f"Please check if appropriate organism[/ID](https://ondemand.hpc.kuleuven.be/ID) type was provided! "
56 f"Allowed proportion ({prop_missing_allowed}) of missing "
57 f"{subset_name} elements exceeded ({prop_missing:.2f}). "
58 f"Too few features from the resource were found in the data."
59 )
---> 60 raise ValueError(msg + f" [{x_missing}] missing from {superset_name}")
62 _logg(f"{prop_missing:.2f} of entities in the resource are missing from the data.", verbose=verbose & (prop_missing > 0))
ValueError: Please check if appropriate organism[/ID](https://ondemand.hpc.kuleuven.be/ID) type was provided! Allowed proportion (0.98) of missing resource elements exceeded (1.00). Too few features from the resource were found in the data. [A2m, Aanat, Abca1, Ace, Ackr2, Ackr3, Ackr4, Actr2, Acvr1, Acvr1b, Acvr1c, Acvr2a, Acvr2b, Acvrl1, Ada, Adam10, Adam11, Adam12, Adam15, Adam17, Adam2, Adam22, Adam23, Adam28, Adam29, Adam7, Adam9, Adamts3, Adcy1, Adcy7, Adcy8, Adcy9, Adcyap1, Adcyap1r1, Adipoq, Adipor1, Adipor2, Adm, Adm2, Ado, Adora1, Adora2a, Adora2b, Adora3, Adra2a, Adra2b, Adrb1, Adrb2, Adrb3, Ager, Agr2, Agrn, Agrp, Agt, Agtr1a, Agtr2, Ahsg, Aimp1, Alb, Alcam, Alk, Alox5, Ambn, Amelx, Amfr, Amh, Amhr2, Ang, Angpt1, Angpt2, Angpt4, Angptl1, Angptl2, Angptl3, Angptl4, Angptl7, Antxr1, Anxa1, Anxa2, Apcdd1, Apln, Aplnr, Aplp1, Aplp2, Apoa1, Apoa2, Apoa4, Apob, Apoc2, Apoc4, Apod, Apoe, Apoo, App, Aqp1, Aqp5, Ar, Areg, Arf1, Arf6, Arpc5, Art1, Artn, Asgr1, Asgr2, Atp1a3, Atp6ap2, Atrn, Avp, Avpr1a, Avpr1b, Avpr2, Axl, Azgp1, B2m, Bambi, Bcam, Bcan, Bdkrb1, Bdkrb2, Bdnf, Bgn, Bmp1, Bmp10, Bmp15, Bmp2, Bmp3, Bmp4, Bmp5, Bmp6, Bmp7, Bmp8a, Bmpr1a, Bmpr1b, Bmpr2, Boc, Bpi, Brs3, Bsg, Bst1, Btc, Btla, Btn1a1, C1qa, C1qb, C1qbp, C1qtnf1, C1qtnf5, C3, C3ar1, C4a, C4b, C5ar1, C5ar2, C920025E04Rik, Cacna1c, Cadm1, Cadm3, Calca, Calcr, Calcrl, Calml3, Calr, Camp, Cap1, Catsper1, Cav1, Ccbe1, Cck, Cckar, Cckbr, Ccl1, Ccl11, Ccl12, Ccl17, Ccl2, Ccl20, Ccl21b, Ccl22, Ccl24, Ccl25, Ccl27b, Ccl28, Ccl4, Ccl5, Ccr1, Ccr10, Ccr2, Ccr3, Ccr4, Ccr5, Ccr6, Ccr7, Ccr8, Ccr9, Ccrl2, Cd14, Cd151, Cd163, Cd177, Cd180, Cd19, Cd2, Cd200, Cd200r1, Cd200r2, Cd200r4, Cd209a, Cd209e, Cd22, Cd226, Cd244, Cd247, Cd248, Cd27, Cd274, Cd28, Cd300lf, Cd34, Cd36, Cd38, Cd3d, Cd3g, Cd4, Cd40, Cd40lg, Cd44, Cd46, Cd47, Cd48, Cd5, Cd53, Cd59b, Cd5l, Cd6, Cd63, Cd68, Cd69, Cd7, Cd70, Cd72, Cd74, Cd79a, Cd80, Cd81, Cd82, Cd86, Cd8a, Cd8b1, Cd9, Cd93, Cdh1, Cdh10, Cdh11, Cdh2, Cdh5, Cdh7, Cdon, Ceacam1, Ceacam16, Ceacam19, Ceacam2, Cel, Celsr1, Celsr2, Celsr3, Cer1, Cfc1, Cfh, Cfp, Cftr, Cga, Cgn, Chad, Chl1, Chrm1, Chrm3, Chrna10, Chrna3, Chrna4, Chrna7, Chrna9, Chrnb2, Chrnb4, Cirbp, Cklf, Clcf1, Cldn4, Clec10a, Clec11a, Clec12a, Clec14a, Clec1b, Clec3a, Clec4g, Cmklr1, Cnr1, Cnr2, Cntf, Cntfr, Cntn1, Cntn2, Cntn3, Cntn4, Cntn5, Cntn6, Cntnap1, Col10a1, Col11a1, Col11a2, Col12a1, Col13a1, Col14a1, Col15a1, Col16a1, Col18a1, Col19a1, Col1a1, Col1a2, Col20a1, Col22a1, Col24a1, Col26a1, Col27a1, Col28a1, Col2a1, Col3a1, Col4a1, Col4a2, Col4a3, Col4a4, Col4a5, Col4a6, Col5a1, Col5a2, Col5a3, Col6a1, Col6a2, Col6a3, Col6a5, Col6a6, Col7a1, Col8a1, Col8a2, Col9a1, Col9a2, Col9a3, Colq, Comp, Copa, Cort, Cp, Cr2, Crh, Crhr1, Crhr2, Crisp2, Crlf1, Crlf2, Crlf3, Crp, Crtam, Csf1, Csf1r, Csf2, Csf2ra, Csf2rb, Csf3, Csf3r, Cspg4, Ctf1, Cthrc1, Ctla4, Cubn, Cx3cl1, Cx3cr1, Cxcl1, Cxcl10, Cxcl12, Cxcl13, Cxcl14, Cxcl16, Cxcl17, Cxcl2, Cxcl5, Cxcr1, Cxcr2, Cxcr3, Cxcr4, Cxcr5, Cxcr6, Cytl1, Dag1, Dcbld2, Dcc, Dchs1, Dclk3, Dcn, Ddr1, Ddr2, Dhh, Dip2a, Dkk1, Dkk2, Dkk3, Dkk4, Dlk1, Dlk2, Dll1, Dll3, Dll4, Dmp1, Dnajb11, Dpp4, Draxin, Drd2, Drd4, Dsc1, Dsc2, Dsc3, Dscam, Dsg1a, Dsg1b, Dsg2, Dsg3, Dsg4, Dysf, Ear11, Ear5, Ebi3, Ecm1, Edil3, Edn1, Edn2, Edn3, Ednra, Ednrb, Efemp1, Efemp2, Efna1, Efna2, Efna3, Efna4, Efna5, Efnb1, Efnb2, Efnb3, Egf, Egfr, Enam, Eng, Enho, Eno1, Enpep, Entpd1, Epgn, Epha1, Epha10, Epha2, Epha3, Epha4, Epha5, Epha6, Epha7, Epha8, Ephb1, Ephb2, Ephb3, Ephb4, Ephb6, Epo, Epor, Erap1, Erbb2, Erbb3, Erbb4, Ereg, Esam, Etv5, F10, F11, F11r, F12, F13a1, F2, F2r, F2rl1, F2rl2, F2rl3, F3, F7, F8, F9, Fabp5, Fadd, Fam3b, Fam3c, Fap, Farp2, Fas, Fasl, Fat4, Fbln1, Fbln2, Fbn1, Fcer1a, Fcer2a, Fcgr3, Fcgr4, Fcgrt, Ffar2, Fga, Fgb, Fgf1, Fgf10, Fgf11, Fgf12, Fgf13, Fgf14, Fgf15, Fgf16, Fgf17, Fgf18, Fgf2, Fgf20, Fgf21, Fgf22, Fgf23, Fgf3, Fgf4, Fgf5, Fgf6, Fgf7, Fgf8, Fgf9, Fgfr1, Fgfr2, Fgfr3, Fgfr4, Fgfrl1, Fgg, Fgl1, Flot1, Flrt3, Flt1, Flt3, Flt3l, Flt4, Fn1, Fndc5, Fpr1, Fpr2, Fras1, Frem1, Frem2, Frs3, Fshb, Fshr, Fst, Fstl1, Fstl5, Fxyd6, Fzd1, Fzd10, Fzd2, Fzd3, Fzd4, Fzd5, Fzd6, Fzd7, Fzd8, Fzd9, Gabbr2, Gad1, Gal, Galp, Galr1, Galr2, Galr3, Gas1, Gas6, Gast, Gc, Gcgr, Gdf1, Gdf10, Gdf11, Gdf15, Gdf2, Gdf3, Gdf5, Gdf6, Gdf7, Gdf9, Gdnf, Gfra1, Gfra2, Gfra3, Gfra4, Gfral, Gh, Ghr, Ghrh, Ghrhr, Ghrl, Ghsr, Gip, Gipr, Gjb2, Glg1, Glp1r, Glra2, Gm11127, Gm13305, Gm13306, Gm2002, Gm2023, Gm2506, Gm3934, Gm5506, Gm7030, Gnai2, Gnas, Gnb3, Gnrh1, Gnrhr, Gp1ba, Gp1bb, Gp49a, Gp5, Gp6, Gp9, Gpc1, Gpc2, Gpc3, Gpc4, Gpc5, Gpha2, Gphb5, Gpi1, Gpnmb, Gpr135, Gpr151, Gpr152, Gpr171, Gpr182, Gpr19, Gpr20, Gpr25, Gpr35, Gpr37, Gpr37l1, Gpr39, Gpr44, Gpr75, Gpr83, Gpr84, Gprc5d, Gprc6a, Grem1, Grem2, Grin2a, Grin2b, Grin2c, Grin2d, Grm1, Grm4, Grm5, Grm7, Grn, Grp, Grpr, Gstm7, Gsto1, Gstp1, Gstp2, Guca2a, Guca2b, Gucy2c, Gucy2e, Gzma, H2-Aa, H2-Ab1, H2-DMa, H2-DMb1, H2-DMb2, H2-Ea-ps, H2-Eb1, H2-K1, H2-M3, H2-Ob, H2-T23, Hapln1, Has2, Havcr2, Hbegf, Hc, Hcrt, Hcrtr1, Hcrtr2, Hdc, Hebp1, Hfe, Hgf, Hhip, Hmmr, Hp, Hpx, Hras, Hrh1, Hrh2, Hrh3, Hrh4, Hsp90aa1, Hsp90b1, Hspa1a, Hspa4, Hspa8, Hspg2, Htr1a, Htr1b, Htr1d, Htr1f, Htr2a, Htr2b, Htr2c, Htr4, Htr5a, Htr6, Htr7, Iapp, Ibsp, Icam1, Icam2, Icam4, Icam5, Icos, Icosl, Ifna11, Ifnar1, Ifnar2, Ifnb1, Ifne, Ifng, Ifngr1, Ifngr2, Ifnk, Ifnlr1, Igdcc3, Igdcc4, Igf1, Igf1r, Igf2, Igf2r, Igfbp4, Igfbpl1, Igfl3, Igflr1, Igsf1, Igsf10, Ihh, Il10, Il10ra, Il10rb, Il11, Il11ra1, Il11ra2, Il12a, Il12b, Il12rb1, Il12rb2, Il13, Il13ra1, Il13ra2, Il15, Il15ra, Il16, Il17a, Il17b, Il17c, Il17f, Il17ra, Il17rb, Il17rc, Il17re, Il18, Il18bp, Il18r1, Il18rap, Il19, Il1a, Il1b, Il1f10, Il1f5, Il1f6, Il1f8, Il1f9, Il1r1, Il1r2, Il1rap, Il1rapl1, Il1rapl2, Il1rl1, Il1rl2, Il1rn, Il2, Il20, Il20ra, Il20rb, Il21, Il21r, Il22, Il22ra1, Il22ra2, Il23a, Il23r, Il24, Il25, Il27, Il27ra, Il2ra, Il2rb, Il2rg, Il33, Il34, Il3ra, Il4, Il4ra, Il5, Il5ra, Il6, Il6ra, Il6st, Il7, Il7r, Il9, Il9r, Iltifb, Impg2, Inha, Inhba, Inhbb, Inhbc, Inhbe, Ins2, Insl3, Insl5, Insr, Irak4, Islr2, Itga1, Itga10, Itga11, Itga2, Itga2b, Itga3, Itga4, Itga5, Itga6, Itga7, Itga8, Itga9, Itgad, Itgae, Itgal, Itgam, Itgav, Itgax, Itgb1, Itgb2, Itgb3, Itgb3bp, Itgb4, Itgb5, Itgb6, Itgb7, Itgb8, Itih2, Izumo1, Jag1, Jag2, Jam2, Jam3, Jmjd6, Kcna3, Kcnd1, Kcnd2, Kcnj10, Kcnj15, Kcnj4, Kcnq1, Kdr, Kel, Kidins220, Kiss1, Kiss1r, Kit, Kitl, Kl, Klb, Klk1b8, Klrb1a, Klrb1b, Klrb1c, Klrc1, Klrd1, Klrg1, Klrg2, Kng1, Kng2, Kremen1, Kremen2, L1cam, LOC100861969, LOC100861978, Lag3, Lair1, Lama1, Lama2, Lama3, Lama4, Lama5, Lamb1, Lamb2, Lamb3, Lamc1, Lamc2, Lamc3, Lamp1, Lamp2, Lck, Lcn2, Ldlr, Leap2, Lefty1, Lefty2, Lep, Lepr, Lgals1, Lgals3, Lgals3bp, Lgals8, Lgi1, Lgi2, Lgi3, Lgi4, Lgr4, Lgr5, Lgr6, Lhb, Lhcgr, Lif, Lifr, Lilrb4, Lin7c, Lingo1, Lipc, Liph, Lman1, Lmbr1l, Lpar1, Lpar2, Lpar3, Lpar4, Lpl, Lpp, Lrig1, Lrig2, Lrp1, Lrp10, Lrp11, Lrp1b, Lrp2, Lrp4, Lrp5, Lrp6, Lrp8, Lrpap1, Lrrc4, Lrrc4b, Lrrc4c, Lrrn3, Lrrtm2, Lsr, Lta, Ltb, Ltbp1, Ltbp3, Ltbr, Ltf, Lum, Ly86, Ly96, Lypd3, Lyve1, Lyz1, Lyz2, Mag, Maged1, Marco, Mas1, Matn1, Mbl2, Mc1r, Mc2r, Mc3r, Mc4r, Mc5r, Mcam, Mcfd2, Mchr1, Mdk, Megf10, Mepe, Mertk, Met, Mfap2, Mfap3l, Mfap5, Mfge8, Mfng, Mfrp, Mgl2, Mgrn1, Mia, Mif, Mmp12, Mmp13, Mmp1a, Mmp2, Mmp24, Mmp7, Mmp9, Mmrn2, Mog, Mpl, Mpz, Mpzl1, Mrap, Mrc1, Mrc2, Mrgprb1, Mrgprb2, Mrgprx2, Msmp, Mst1, Mst1r, Mstn, Mtnr1a, Mtnr1b, Mttp, Muc2, Muc5ac, Muc6, Musk, Myl9, Myoc, Nampt, Ncam1, Ncam2, Ncan, Ncl, Ncr1, Ncstn, Ndp, Negr1, Nell2, Neo1, Nfasc, Ngf, Ngfr, Nid1, Nlgn1, Nlgn2, Nlgn3, Nmb, Nmbr, Nms, Nmu, Nmur1, Nmur2, Nodal, Notch1, Notch2, Notch3, Notch4, Npb, Npbwr1, Npff, Npffr1, Npffr2, Npnt, Nppa, Nppc, Npr1, Npr2, Npr3, Nps, Npsr1, Nptx1, Nptx2, Nptxr, Npvf, Npw, Npy, Npy1r, Npy2r, Npy5r, Nr0b2, Nrcam, Nrg2, Nrg3, Nrg4, Nrp1, Nrp2, Nrsn1, Nrtn, Nrxn1, Nrxn2, Nt5e, Ntf3, Ntf5, Ntn1, Ntn3, Ntn4, Ntng1, Ntng2, Ntrk1, Ntrk2, Ntrk3, Nts, Ntsr1, Ntsr2, Nucb2, Nxph1, Nxph2, Nxph3, Ocln, Ogfr, Oit1, Olfm2, Olr1, Omg, Oprd1, Oprk1, Oprl1, Oprm1, Orai2, Osm, Osmr, Ostn, Oxt, Oxtr, P2rx7, P2ry12, P2ry14, P2ry6, P4hb, Pam, Pard3, Pcsk1n, Pcsk9, Pdap1, Pdcd1, Pdcd1lg2, Pdcd2, Pdgfa, Pdgfb, Pdgfc, Pdgfd, Pdgfra, Pdgfrb, Pdpn, Pdx1, Pdyn, Pecam1, Penk, Pf4, Pgf, Pglyrp1, Phex, Pi16, Piga, Pigf, Pigr, Pip, Pirb, Pkm, Pla2g10, Pla2r1, Plat, Plau, Plaur, Pld1, Pld2, Plg, Plgrkt, Plscr1, Plscr4, Pltp, Plxdc1, Plxdc2, Plxna1, Plxna2, Plxna3, Plxna4, Plxnb1, Plxnb2, Plxnb3, Plxnc1, Plxnd1, Pmch, Pnoc, Podxl2, Pomc, Postn, Ppy, Prl, Prlh, Prlhr, Prlr, Prn, Prnd, Proc, Procr, Prok1, Prok2, Prokr1, Prokr2, Pros1, Prss2, Prtg, Psap, Psen1, Pspn, Ptch1, Ptch2, Ptdss1, Ptgdr, Ptger2, Ptger3, Ptger4, Ptgir, Ptgs2, Pth, Pth1r, Pth2, Pth2r, Pthlh, Ptk7, Ptn, Ptpn6, Ptpra, Ptprb, Ptprc, Ptprf, Ptprg, Ptprj, Ptprk, Ptprm, Ptprr, Ptprs, Ptpru, Ptprz1, Pyy, Qdpr, Qrfp, Qrfpr, Ramp1, Ramp2, Ramp3, Rarres1, Rarres2, Rbp3, Rbp4, Reck, Reln, Ren1, Ret, Retn, Rgma, Rgmb, Rhag, Rhbdf2, Rhbdl2, Rims1, Rims2, Ripk1, Rln1, Rln3, Rnf43, Robo1, Robo2, Robo3, Robo4, Ror1, Ror2, Rps19, Rpsa, Rspo1, Rspo2, Rspo3, Rspo4, Rtn4, Rtn4r, Rtn4rl1, Rxfp1, Rxfp2, Rxfp3, Rxfp4, Rxra, Ryk, Ryr1, Ryr2, S100a1, S100a10, S100a4, S100a8, S100a9, S100b, S1pr1, S1pr2, S1pr3, S1pr4, S1pr5, Saa1, Saa2, Scara5, Scarb1, Scarf1, Scel, Scgb1a1, Scgb3a1, Scgb3a2, Scn5a, Scn8a, Sctr, Scube2, Sdc1, Sdc2, Sdc3, Sdc4, Sdk2, Sectm1a, Sele, Sell, Selp, Selplg, Sema3a, Sema3b, Sema3c, Sema3d, Sema3e, Sema3f, Sema3g, Sema4a, Sema4b, Sema4c, Sema4d, Sema4f, Sema4g, Sema5a, Sema5b, Sema6a, Sema6b, Sema6d, Sema7a, Serpina1a, Serpina1b, Serpina1c, Serpina1d, Serpina1e, Serpina7, Serpinc1, Serpine1, Serpine2, Serpinf1, Serping1, Sertad1, Sfrp1, Sfrp2, Sftpa1, Sftpd, Shank1, Shank2, Shbg, Shh, Sigirr, Siglec1, Sirpa, Slamf9, Slc16a1, Slc16a2, Slc16a7, Slc17a7, Slc18a2, Slc18a3, Slc2a2, Slc37a1, Slc40a1, Slc4a11, Slc6a8, Slit1, Slit2, Slit3, Slitrk1, Slitrk2, Slitrk3, Slitrk6, Slpi, Slurp1, Smap1, Smo, Snca, Snx14, Socs2, Sorbs1, Sorcs2, Sorcs3, Sorl1, Sort1, Sost, Sostdc1, Sparc, Spink3, Spint1, Spn, Spon1, Spon2, Spp1, Sptan1, Sptbn2, Sst, Sstr1, Sstr2, Sstr3, Sstr4, Sstr5, St14, St6gal1, Stab1, Stab2, Stra6, Stx1a, Stx3, Stx4a, Tac1, Tac2, Tacr1, Tacr2, Tacr3, Tarm1, Tbxa2r, Tcn2, Tctn1, Tdgf1, Tecta, Tectb, Tek, Tff1, Tff2, Tff3, Tfpi, Tfr2, Tfrc, Tg, Tgfa, Tgfb1, Tgfb2, Tgfb3, Tgfbr1, Tgfbr2, Tgfbr3, Tgm2, Tgs1, Thbd, Thbs1, Thbs2, Thbs3, Thbs4, Thpo, Thy1, Tie1, Timp1, Timp2, Timp3, Tln1, Tlr1, Tlr2, Tlr4, Tlr6, Tlr7, Tlr9, Tmed5, Tmem219, Tmem67, Tnc, Tnf, Tnfrsf10b, Tnfrsf11a, Tnfrsf11b, Tnfrsf12a, Tnfrsf13b, Tnfrsf13c, Tnfrsf14, Tnfrsf17, Tnfrsf18, Tnfrsf19, Tnfrsf1a, Tnfrsf1b, Tnfrsf21, Tnfrsf25, Tnfrsf4, Tnfrsf8, Tnfsf10, Tnfsf11, Tnfsf12, Tnfsf13, Tnfsf13b, Tnfsf14, Tnfsf15, Tnfsf18, Tnfsf4, Tnfsf8, Tnn, Tnr, Tnxb, Tph1, Tpo, Tpsb2, Tradd, Traf2, Traf3, Trem1, Trem2, Treml2, Trf, Trh, Trhr, Trpm2, Trpm3, Trpv1, Trpv6, Try10, Try4, Try5, Tshb, Tshr, Tslp, Tspan1, Tspan10, Tspan12, Tspan14, Tspan15, Tspan17, Tspan5, Ttr, Txlna, Tyro3, Tyrobp, Ucn, Ucn2, Ucn3, Unc5a, Unc5b, Unc5c, Unc5d, Uts2, Uts2b, Uts2r, Vangl2, Vasn, Vasp, Vcam1, Vcan, Vcl, Vegfa, Vegfb, Vegfc, Vgf, Vim, Vip, Vipr1, Vipr2, Vldlr, Vsig10l, Vtn, Vwf, Wfikkn2, Wif1, Wnt1, Wnt10a, Wnt10b, Wnt11, Wnt16, Wnt2, Wnt2b, Wnt3, Wnt3a, Wnt4, Wnt5a, Wnt5b, Wnt6, Wnt7a, Wnt7b, Wnt8a, Wnt8b, Wnt9a, Wnt9b, Xcl1, Xcr1, Ybx1, Znrf3, Zp3, a] missing from var_names
Hi @soniyalama,
Given that LIANA does not find those genesymbols, it might be best to check that your adata.var.index
contains them.
re running connectome: they key_added
adds the results dataframe to the adata.uns[key_added]
slot, you should use the connectome method (also imported in the tutorial) to run connectome.
Hi @dbdimitrov,
Thank you for your reply.
Well, we've checked for overlap between both the mouse consensus genes and my own genes and there is an overlap of 1203 genes. So I'm not sure what is creating the issue here?
Kind regards,
Soniya Lama
So my dataset contains 15 723 unique genes. The mouseconsensus data which I checked via this code: "mouseconsensus = li.resource.select_resource('mouseconsensus')
contains 7978 genes in total, where 1741 are unique.
I did check the overlap which gave me 1203 genes. If you do 1203/7978 that is already 15% of the resource. Now I don't get why the error Is saying that I have 0% overlap between both my adata.var_names and my mouseconsensus?
Am I looking at the mouseconsensus in a wrong way in any way?
Thanks in advance,
Soniya Lama.
Hi @soniyalama, this is strange - if the var_names
overlap with the resource, it should work. I could double-check if you provide a small subset of your data.
I can't seem to insert a .h5ad format here. I sent it through mail.
Thanks for your help!
Hi @soniyalama,
It seems like you are passing the .raw instead of X, and your .raw adata has numbers instead of gene names in .var
.
It should work if you pass use_raw=False
:
li.mt.cellphonedb(adata, groupby='group_label', expr_prop=0, resource_name='mouseconsensus', verbose=True, use_raw=False)
I plan to change use_raw
to be False by default in future version as it seems now that the preferred approach is just using layers. Hope this helps.
Hi Mr. Dimitrov,
This seems to resolve the issue. Thanks a lot. Another question I had if it's correct that the tool is running on the SCT assay, layer = counts, or layer = data? This wasn't specified, and I'm not pretty well known.
Kind regards,
Soniya Lama.
@soniyalama as long as the cell distributions are normalised it should be fine. I can't recall if SCT counts were non-negative though, I assume yes, and their residuals are the mean-normalised ones?
Either way, comparable cell distributions and non-negative counts would work with liana :)
Hope this helps.