Closed spietrzak closed 2 years ago
rcorces
commented
3 years ago This is the same issue posted here: https://github.com/GreenleafLab/ArchR/discussions/762 I'm not sure what the problem is but perhaps you can provide more context. What version of ComplexHeatmap are you running?
spietrzak
commented
3 years ago It is version 2.2.0. Everything should be the same as my previous ArchR R-projects since I haven't downloaded anything new or updated any packages, which is why I was confused by this error.
rcorces
commented
3 years ago What does heatmapGS look like? does it look normal?
spietrzak
commented
3 years ago Here's what it looks like when I just run heatmapGS:
> heatmapGS
$mat
Serpinb6b Ptk2b Serinc3 Ccl11 Ccl12 Ctla2b Ch25h Cd53 Evi2b
Wfdc17 Wfdc18 Mir7681 Evi2 Evi2a Cd300c Sla 2310008N11Rik Ly9
Car6 Ccr3 C3ar1 Olfr111 Lilrb4a Hk3 Mir6353 Inpp5d Dgkd
Gm19582 Ugt1a10 Steap3 Il10 Mapkapk2 Ctse Rab7b Rnpep Gm15850
Rgs1 Pla2g4a Cd244a Slamf7 Mir7683 Cd48 Cd84 Aim2 1700016C15Rik
1700112H15Rik D730003I15Rik Zc3h12d Mir5104 Sash1 Adgb Ccdc28a 1700020N01Rik
Raet1a Raet1c Raet1d C920009B18Rik Stx7 Slc16a10 Man1a Pkib Kif1bp
Itgb2 Poc1b Osbpl8 Glipr1 Lyz2 Lyz1 Gns Lrp1 Osm
Ikzf1 Plek D630024D03Rik Stk10 Kcnmb1 Lcp2 Havcr2 Rnf130 Lyrm7os
Nlrp3 Cdrt4os1 Pmp22 Gas7 Tnfsfm13 Scimp Ssh2 Ccl2 E230016K23Rik
Ccl3 Mir142 Tspoap1 Mir142b Gm11541 1700003D09Rik Grn Map3k14 Milr1
Cd300a Cd300lb Cd300ld Cd300c2 Tmem104 Nat9 Cyth1 Hs1bp3 Rhob
Slc7a15 Pik3cg Prkch Riox1 Batf Cep128 Gpr65 Kcnk13 Lgmn
Serpina3c Adssl1 Pld4 1110046J04Rik Cd83 Rnf144b A930002C04Rik Susd3 Fgd3
Tifab Tgfbi Mef2c Lhfpl2 Cd180 Plau Prkcd Stab1 Tmem273
Arhgap22 Ptger2 Slc7a8 4930556J02Rik Ctsb Dok2 2410012E07Rik Rubcnl
Lcp1 Dnajc15 4933432I03Rik Acod1 1700100I10Rik Rap2a Ubac2 Gpr183 Timm8a2
Dab2 C9 Otulinl Mir6951 2310043O21Rik AU022793 Trps1 Nsmce2 Gm19510
Tg St3gal1 Mir1942 Ncf4 Csf2rb Rac2 Cyth4 Mkl1 Cerk
Yaf2 Gtsf2 Nckap1l Snx29 Marf1 Klhl6 Adipoq C730014E05Rik St6gal1
BC106179 Nrros Bex6 Ccdc54 St3gal6 4930529L06Rik App Gm10791 1600002D24Rik
Atp6v0c Clic1 Lta Mir6974 Tnfrsf21 Cnpy3 Trem1 Trem2 Adgre1
Lpin2 Mir187 Bin1 E230025N22Rik Mospd4 Snx24 Csf1r Mir6983 F830208F22Rik
Ehd1 Fermt3 Fth1 Dagla Slc15a3 Ms4a7 Ms4a6b Pfpl Mpeg1
Lpxn 4930554I06Rik A1cf Entpd1 Pik3ap1 Shtn1 Prkcq Tmem236 Mrc1
4930426L09Rik Itga4 Olfr1226 Dgkz Mir6999 Slc1a2 D330050G23Rik Patl2 Il1b
Sirpa Slc23a2 Rin2 Abhd12 Ccm2l Hck Tgm2 9130015L21Rik
Gm826 Neurl2 Slc13a3 Trp53rkb Tmem189 Ptpn1 Tpd52 Gm9833 Nceh1
Mir3092 Il2 Il21 Slc7a11 P2ry13 P2ry12 Fnip2 Etv3 Ctsk
Ctss Plekho1 Fcgr1 Gm5544 Cd101 Cttnbp2nl Tmigd3 Adora3 Mir760
Gbp2b Gbp2 Mcoln2 2210414B05Rik Lyn Cyp7a1 Bach2os Cd72 Coro2a
Hacd4 Ago3 Laptm5 Ptafr Themis2 Ubxn11 C1qb Atp13a2 Efhd2
Tnfrsf1b Cd36 Slc35f6 Sh3bp2 Tbc1d14 Slc2a9 Tlr6 Rbm47 Tec
Enam Jchain Cxcl2 Anxa3 Gm8013 Cmklr1 Ncf1 Pilra
C130050O18Rik Gna12 Daglb Irf5 Plxna4os1 Clec5a Gpnmb Snx10 Hpgds
Tnip3 Arhgap25 4930512J16Rik Chchd6 Mitf Mir7043 Tmem72 Il17ra Apobec1
Clec4a1 Clec4a3 Clec4a2 Clec4d Vmn2r27 1700027F06Rik Clec12a Ptpro
4930479D17Rik Lair1 C5ar1 B9d2 Tgfb1 Zfp36 Tyrobp Usf2 Fxyd5
Mir7050 Cebpg Cebpa Cd33 Ptpn5 Cyfip1 Mef2a Gm21057 Furin
Gm15880 Tm6sf1 P2ry6 P2ry2 Trim30a Rnf141 Il21r Itgam Itgax
Rgs10 Abraxas2 6430531B16Rik Adam8 Mir7062 Cln8 Adam3 Mfhas1 Msr1
Ell Il15 Mir27a Mir24-2 Adcy7 Nod2 Wwp2 Pkd1l2 Cotl1
6430548M08Rik Irf8 A630001O12Rik Nrp1 Mir1903 Mmp13 Fat3 Fli1 Clmp
Ubash3b BC049352 Mir7086 Tmprss13 Cadm1 1110032A03Rik Cd276 Hexa
Gm5122 Smad3 Plekho2 Cox7a2 Tbc1d2b Usp4 Ccrl2 Cmtm6 Tgfbr2
Cx3cr1 Lyzl4 Lyzl4os Xcr1 Ccr1 Ccr2 Cybb Atp2b3 Stard8
Sat1 Ptchd1 Tmsb4x Tlr8 Prl3d1 Vmn1r43 Ppifos Orm2 Gm15638
Gm14137 D830026I12Rik Apol9b Ptgs2 Vmn2r81 Krtap4-16 AF357425 4930544M13Rik Cst6
Lce1l Nppa Ppbp U90926 Fam71f1 Siglece 4933405O20Rik Hspb2 Mir6386
Ucn2 Olfr482 Olfr481 Snord89 Ccl7 Gm11937 Krtap2-4 E330017A01Rik Kcnk7
Ms4a4b Ms4a6c Olfr1426 1700025M24Rik Olfr298 4930505K13Rik Olfr148 Ssxb5 Gm9159
4732490B19Rik BC021767 Klk1b24 Olfr522 Mir411 E030030I06Rik Gm13648 Mir429 3830432H09Rik
Arhgap45 4930404N11Rik Mir7211 Rdh18-ps 0610009B22Rik Slc36a3 Krt40 Mir770 Mir6943
Il17rb Rnase9 Olfr168 B230307C23Rik Tff2 Gstp2 Olfr1443 Kyat1 Selenbp2
Kncn Oxct2b Rnf223 Pf4 Cxcl3 Depp1 C1s2 BC064078 Pirb
Cyp2b23 Selenov Ush1c Olfr504 Rps25 Tac2 Olfr96 Opalin Mir103-2
Cst13 Ankub1 Mup10 8030455M16Rik Crtam Tmprss5 Sh2d7 Dgat2l6 Gcgr
Vmn1r219 Rnase1 Gsdmc2 1700066B19Rik 0610031O16Rik Adh7 Gm15421 Tmem89 Bgn
Col3a1 Wisp1 Cxcl9 Serpine1 Fmo6 Ifi27l2b 4933412O06Rik Ear14 Ms4a2
Gm10220 Tmem204 Fgf2 C1qtnf7 Krtap3-1 4930447A16Rik Mir1941 Fam180a Spata4
Mir802 Sbsn Mir346 Mir30a Serpinb11 4930463O16Rik Timp3 Dcn Rdh1
Mettl7b Tlcd2 Fam117a Smim5 Cep295nl Zc2hc1c Vmn1r199 Serpinb9 Mir3075
Ccdc122 Cyp11b1 Mlc1 E130310I04Rik Upk1b Cd200 Msln Slc25a27 Gata6
Gm15328 A930001C03Rik Myrf E030003E18Rik Aldh1a1 Pnlip Olfr996 Wt1os Wt1
Trim69 Erv3 Angpt4 Gucy1a1 Mir7010 Sprr4 Gpr88 Tnfsf15 Rspo1
Mir3969 Stbd1 Upk3b 1700065J11Rik Hoxa4 6430584L05Rik Gm10400 1700034J05Rik Siglecg
Bnc1 Mical2 Tmem255b Dctn6 4930567H12Rik Tagln Tex12 Loxl1 Gm20745
Tmem108 Krtap1-4 Foxs1 Carmn 4930431F12Rik Uroc1 Serpina16 Il1r1 Il1rl1
Gm8883 Dnm3os Mir29b-2 Lum 4930473O22Rik Col1a1 Prl6a1 Aspn Defb43
D630010B17Rik 1600019K03Rik Zfp474 1700034E13Rik Dbh Col5a1 5430434I15Rik Postn Tnc
Cxcl15 Slc10a6 Col1a2 Lsp1 Vmn1r185 Nlrp9a 4933413L06Rik 4930591A17Rik Lbhd2
Olfr266 Il1rl2 4933417E11Rik Tnp1 Kcne4 Twist2 C230024C17Rik Rgs16 Tnfsf18
Fmo3 Grem2 Mir29c Raet1e H60b Casp14 Epyc Mir6920 Mfap4
Gm12295 Vps53 Gm53 Mir196a-1 Krtap4-7 Gm11568 Gm11559 Krtap9-1 Gm38407
Serpina3b Serpina3g 6430411K18Rik Mir434 Mir432 Rtl1 Mir136 Rian AF357426
DQ267101 AF357355 DQ267102 Mir882 Mir379 Mir299a Mir380 Mir1197 Mir323
Mir758 Mir329 Mir494 Mir679 Mir299b Mir1193 Mir666 Mir543 Mir495
Mir667 Prl3d2 Prl3d3 4930486L24Rik Ctla2a Adamts16 Gm10248 Cma1 4933402J15Rik
Mir30b Mir155hg Mir155 4930590A17Rik 4930474M22Rik Thbs2 H2-M9 Olfr99 Olfr101
Spink14 Pdgfrb Mir143 Olfr1505 Anxa1 Pgm5 Gm23363 Mir199b Fap
Olfr1016 Gm13985 Thbs1 Fam217b Fam198b Sprr2k Sprr3 Gm12440 Adh1
Mir876 BB031773 Gngt1 Rnf133 Cald1 Ptn 4931430N09Rik Tmem52b Mir344d-1
Mir344d-2 Mir344d-3 Gm16157 P4ha3 Olfr549 Trim34b Adam18 1600027J07Rik Mir199a-1
Olfr151 Olfr957 Olfr983 Mirlet7a-2 Ankk1 4933407I05Rik Uchl4 Col12a1 Srpx
Zfp300 Tle6 Krtap1-5 Defb47 1700119H24Rik 4930524O05Rik Cpa1 Mgp Mir6345
Nepn Loxl2 Mir6950 Mettl7a3 Mir6367 Fpr1 Tpsg1 Abcg5 Fabp9
Orm3 Npvf Tgfb1i1 Mir100 H2al1n Gm31641 Kcnj15 Krt79 Mir6985
Mir133b Col5a2 Crygf 2810442N19Rik Ifi207 Ifi205 Aig1 Calhm4 Mir3966
Kera 4930579P08Rik Gm5431 Gm12185 1810065E05Rik 4930504O13Rik Olfr30 Olfr325 Gm11544
Krt26 Gm11563 Msgn1 Mir680-3 1810007C17Rik Ifi27 Ifi27l2a Serpina1f Serpina3a
Serpina3f Gm2721 3110009F21Rik Omd A530065N20Rik Zfp456 5430425K12Rik 4930405A10Rik
Mir7210 Lrtm1 4930503F20Rik 9330188P03Rik Gm15941 Baalc Rspo2 Gm20740 Csf2rb2
Il2rb Adamts5 Cldn20 Olfr239 Stard4 Lox Slc14a1 Glis3 Lipm
Itih2 Adamtsl2 Arhgap15os Hoxd12 Tmem239 Wisp2 Wfdc8 Spint4 Mir6340
Mir466q Gm6634 Ngf Aknad1 Gm16325 Ptgfr Musk Col27a1 Mir455
Tnfsf8 Tlr4 Ifnb1 Gm13290 LOC106557447 Mir31 Wincr1 Tmprss11c Cxcl5
Cxcl1 Mepe Gm7538 Gng11 Cav1 Gm2663 2210010C04Rik Clcn1 Svs1
Vmn1r44 Rdh8 Layn Cyp8b1 Mir5617 Rhox2f Xlr4a Rtl3 Mir7094-2
Cyp3a41a Pnck Vmn2r121 4930524N10Rik Samt2 Timd2 Mepce 4921511C20Rik Tex13a
4921511M17Rik Krt6b Samt4 Sva Vmn2r102 Sult2a1 Scgb1b20 Slx Mbd6
Ddit3 Mapk7 Lrrc46 Mrpl10 Mir8101 Tmc6 9430083A17Rik Snord69 Snord19
Phf7 Bap1 LOC105245869 Derl1 Phf5a Zbtb12 Olfr107 Olfr110 Olfr135
Esp18 Olfr1461 Olfr344 Olfr1212 4933434E20Rik Lce1j 4930539J05Rik C87499 Ifna13
Cyp2j11 Gpbp1l1 BC005561 1110006O24Rik Vmn1r26 Polr2i Ovol3 Tmem147 Scgb1b3
Scgb2b21 Mrgpra1 Mrgpra2a Mrgpra3 Mrgprx2 Anapc15 Usp17le Sh2b1 Samd1
Olfr25 Senp8 Myo9a Fbxw18 Efhc2 Gm4297 Gm5168 Gm14625 Gm14692
Gm14744 5430402E10Rik 1700084M14Rik Mageb18 4933401B06Rik Gm382 Cldn34c4 9430007A20Rik
2810047C21Rik1 Olfr812 Gm6614 Olfr771 Olfr777 Olfr780 Olfr796 Olfr805 Adam6a
Gm10732 Oog3 Gm13124 Cyp3a25 Olfr46 Olfr804 Mir8105 Olfr768 Olfr776
Olfr788 Olfr790 Olfr791 Olfr801 Olfr808 Olfr810 Olfr811 Olfr814 Olfr822
Olfr824 Mir7094-1 Mir6388 Gm5478 Krt74 Aaas Hoxc13 Hotair Hoxc10
Mir196a-2 Hoxc9 Hoxc5 Mir615 Hoxc4 Mucl1 Cbln2 Bpifa3 Sycp2
B230312C02Rik Mir133a-2 Birc7 9130204L05Rik Mir3963 Gm20752 Aadacl3 Gm4736 Gm8882
Prp2 B230110G15Rik Slco1a4 Slco1a6 1700015G11Rik Nkx6-2 5830411N06Rik Olfr527
Olfr60 Olfr530 Olfr532 Olfr533 Olfr538 Muc5b Ccdc7a Gm16445 Olfr794
Olfr792 Olfr802 Olfr813 Adam6b Olfr1307 Vmn2r68 Magea2 Gm5415 Slc26a9
Apcs Sertad4 4930503O07Rik Sf3a2 Plekhj1 Sgta 4930503E24Rik Rdh19 Mip
Timeless Olfr763 Olfr765 Olfr809 Olfr815 Olfr1383 2810408A11Rik Olfr59 Gm11538
Taco1 Nup85 Tspan10 Aspscr1 Serpina1a B930059L03Rik Abt1 Btn1a1 Hist1h4h
Cts8-ps 4930434J06Rik Zfp641 Olfr285 Gm5475 Galnt6 Krt87 Gm6042 Krt71
Krt2 Krt76 Hoxc8 Hoxc6 1700123O21Rik Krtap8-1 Igsf5 Itgb2l Pcp4
4933400B14Rik Gm4719 Dpf2 Bpifb6 Bpifb3 Bpifa6 Bpifa2 Wfdc13 Edn3
Chrna4 Olfr1331 Olfr1330 Gm13178 Sdf4 B3galt6 Ambn Triap1 C330018A13Rik
Nsun5 4930587E11Rik Slc6a11 Mug1 Klri1 A630073D07Rik Rergl Kras Med21
Olfr586 Gm4759 Olfr497 Pdilt Olfr531 Olfr536 Muc5ac Krtap5-2 Ifitm10
Ins2 Th Exoc8 Sprtn Fbxw20 Fbxw26 Tgm4 Ccr1l1 Btbd35f7
Olfr1324 Gm16404 3830403N18Rik Gpr101 Tslrn1 Magea10 Fam47c Mageb4 Gm44
Mageb2 Gm5072 1700010D01Rik Heph Gm5166 Dmrtc1a Mir384 H2afb2 4930558G05Rik
Pramel3 Kir3dl2 Plp1 Gm5643 Mir1298 Gm15085 Gm15127 Luzp4 Gm15097
Cldn34a Gm10057 4930503H13Rik Smpx Grpr Asb11 Asb9 Glra2 Frmpd4
Arhgap6 Amelx Prr23a3 4930433N12Rik Olfr816 Slc39a4 BC080695 Gm13083 Pramef17
Pramef12 Syna Vmn2r44 Ceacam12 Usp17lc Olfr503 Prr23a2 Tas2r114 Usp17lb
Mir3073a Slc22a28 4930430A15Rik Gm13078 Tas2r110 Cdhr5 Prr23a1 Olfr782 Pcdhb4
Krt17 Tmprss12 Vmn2r113 Umod Camsap3 Olfr247 Olfr820 Neurod4 Pycr1
Olfr744 Olfr745 Olfr1186 Olfr1238 Hsd3b4 Olfr553 Olfr609 Cd163l1 Olfr1406
Olfr770 Olfr773 Olfr774 Olfr781 Olfr823 Olfr827 Htr1a Olfr164 Vmn2r108
Olfr1469 Olfr1184 Olfr1243 Olfr1300-ps1 Sis Amy2b Gm12886 Gm13103 C87977
Pramel5 Gm13128 Mir200a Cyp3a11 Cyp3a59 Vmn2r19 Klra7 Tas2r107 Tas2r117
Tas2r103 Gm5886 4922502N22Rik Vmn1r73 Olfr479 Gpr139 Cd209e Cd209b Olfr847
Myadml2 Dio3os Olfr1232 Lce1k Gm1979 Mir7058 Gm2042 Gm21319 BB287469
Gm20767 AF067061 Ptf1aos Olfr1166 6430503K07Rik Igsf21 Olfr474 Hmx2 Utf1
Olfr61 Sox1ot Sox1 Adad2 Grin3b Olfr825 Olfr826 Vmn1r204 Klhdc7b
Dhh Six3os1 Six3 St8sia3 Olfr1431 Zfp442 Gm14327 E130018O15Rik Hmx1
4930572K03Rik Klra17 Klra5 Slco1b2 Olfr603 Olfr658 Tmem59l Ccdc7b Gm16701
Olfr1408 Olfr218 Olfr429 D1Pas1 Olfr1354 Olfr8 Fgf22 Onecut3 Gadd45b
Diras1 Ccer1 Kcnmb4os2 March9 Cdk4 Slc26a10 Arhgap9 Stac3 Ndufa4l2
Shmt2 Gpr182 Rdh16 Rdh7 Ikzf4 Gm26876 Olfr769 Olfr786 Olfr789
Olfr799 Olfr818 Tespa1 Vmn2r84 Vmn2r86 Lhx1 Lhx1os Hoxb8 Hoxb7
Hoxb5os Hoxb6 Hoxb5 Mir10a Hoxb4 Hoxb3 Pnmt Ppy Pyy
Trim80 Mir3968 Evpl Qrich2 Prpsap1 Cygb Prcd St6galnac1 BC018473
Rbfox3 Nptx1 Gm11762 Mir338 Notum Uts2r Dio3 Mir1247 Amn
Mir203 Vmn1r205 Ddx4 Mir449b Mir449a Hcn1 Olfr739 Hs6st3 1700006F04Rik
Zic5 Gm5144 Scrt1 B230214G05Rik Miox Odf3b Spn-ps H1fnt Olfr281
Wnt1 Ddn Prph Dnajc22 Kcnh3 Aqp5 I730030J21Rik Scn8a Fignl2
Ankrd33 Krt72 Krt4 Hoxc12 Hoxc11 Krtap16-3 Krtap20-2 Olig2 Olig1
Lrg1 Pcdhb7 Slc22a27 Olfr1484 Pnliprp2 Vax1 Kcnk18 Gm7102 Haglr
Olfr1118 Olfr1120 Olfr1130 Olfr1173 Olfr1211 Olfr1228 Olfr1240 Mdk Olfr1275
Olfr1294 Nkx2-2 Sun5 Bpifb4 Myh7b Mir499 Slc32a1 9430021M05Rik Kcns1
Cd40 Ripor3 1700028P15Rik Cbln4 Ctcfl Ctcflos Zbp1 Ankrd60 Gm10714
Lsm14b Gata5 Gata5os Mir1a-1hg Mir1a-1 Bhlhe23 Kcnq2 Eef1a2 Ppdpf
Ptk6 Helz2 Slc2a4rg-ps Abhd16b Lkaaear1 Mir3093 Lce1h Hfe2 Itga10
Tacr3 AI606473 Acnat1 Foxd3 Skint10 2610028E06Rik CK137956 Csmd2os Tmem200b
Zfp593 Gm13032 4930515B02Rik Gm13023 Gm13084 Pramef25 Pik3cd Gpr157 Slc2a7
Hes2 Gm833 Ajap1 5930403L14Rik Actrt2 Hes5 Plch2 Tmem52 Mir200b
Perm1 Plekhn1 Abcg3 Lhx5 Tmem132d Piwil1 Rhbdd2 Pop7 1700123K08Rik
4930500L23Rik Uncx Cyp3a44 Gsx1 Plut Cdx2 4930505K14Rik Rxfp2 Zar1l
Vmn2r18 Gimap9 Gimap5 Vmn1r14 Egr4 Vmn1r53 4921513H07Rik Gm156 Klra22
Klra4 Klra12 Klra15 Klra9 Klra13-ps Klra1 Tas2r106 Prb1 Prpmp5
Prh1 Tas2r121 Tas2r102 Tas2r116 Tas2r125 Tas2r109 Tas2r140 Kap Gm30332
Slco1a1 Rps4l Vmn1r57 Nlrp2 Olfr1347 Ppm1n Eid2b Pth2 Izumo1
Olfr305 Olfr615 Gp2 Hs3st2 Doc2a Sez6l2 Asphd1 Hmx3 4930543N07Rik
Msx3 Olfr525 Olfr53 Syce1 Cox8b Pkp3 Sct Drd4 Tollip
Brsk2 Mir3104 Igf2 Igf2os Mir483 Cdkn1c Phlda2 Adam29 Hapln4
Gdf1 Crlf1 Mir7240 Kcnn1 1700026F02Rik Mir6769b 2210011C24Rik Mir1199 Ces1d
Ces2h Plekhg4 Gfod2 Gm10280 Syce1l Hsdl1 Dnaaf1 Kcng4 Fendrr
Foxf1 Foxc2 1700018B08Rik Jph3 Cyba Cbfa2t3 Cdh15 Spg7 Dpep1
Chmp1a Vps9d1 Spire2 Mc1r Tubb3 Gas8 Ccsap Agt Trim67
Map3k21 Slc35f3 Rgl3 Foxl2os Iqcf3 Fam240a Susd5 Mir467h Eomes
Acaa1b 4930593C16Rik Cck 9530059O14Rik Slc6a20a Nlrp4g Zfp711 4932411N23Rik Pramel6
Gm14139 Gm2381 Vmn1r226 Gm14124 Zscan4a Olfr132 Cyp2c54 Olfr341 Olfr1126
Pramel7 Olfr153 C130073F10Rik Pramef6 Speer4a Gm10471 Zscan4d Vmn1r72 Vmn1r83
Ceacam5 Apoc1 Vmn2r63 Mrgprb2 Olfr867 Gm3434 Olfr893 Olfr978 Mir200c
Vmn2r28 Gm3285 Car4 Gm10436 4930467E23Rik Pigr Il24 Tmem81 Chil1
Fcer1g 1700009J07Rik Mir6410 1700030O20Rik Rdh16f2 Prim1 Gm11985 Gm4926 Cldn7
Slfn2 Gm11545 Tmem92 Gm11564 Smim6 Gm8300 Gm7104 Serpinb6c Gm8016
Mir6947 Vmn2r89 Mir6241 Mir7212 Krt8 Krt18 Olfr194 Krtap6-5 Mrap
A230009B12Rik Vmn1r227 Vmn1r229 H2-Q4 H2-M2 Olfr124 Vmn1r238 Ttr 4933408B17Rik
Taf7 Pcdh12 Scgb3a2 2210404E10Rik Olfr1457 Olfr1459 Olfr1465 Pkd2l1 Mir669d-2
Mir467c Mir466b-1 Mir669a-3 Mir669g Obp2a Mir181a-2 Tfpi Olfr1124 Olfr1141
Olfr1158 Olfr1176 1700029I15Rik Olfr1283 8030411F24Rik Dynlrb1 Tchhl1 Tdpoz3 Gm10696
Sv2a Ifnk Gm35073 Gm12794 Lin28a Mir7018 Pramel4 Pramef20 1700012P22Rik
Slc34a2 9130230L23Rik Gm19583 Vmn2r13 Olfr448 Olfr447 4921529L05Rik Vmn1r15 Gm1070
1700072O05Rik Klrc1 Zscan4c Zscan4f Vmn1r87 Vmn1r88 Obox6 Psg19 Ckm
Vmn1r184 2200002D01Rik Pmis2 2200002J24Rik C86187 Gm9999 Mir344h-1 Olfr299 Folr1
Olfr576 Olfr577 Olfr582 Usp17ld Olfr596 Trim6 Usp17la Aqp8 Ctf2
Prr33 Tnnt3 Trim60 Olfr374 Ctrb1 Mir7076 Olfr26 Mir5626 Rhox5
Rhox6 Rhox7a Rhox8 Dusp9 Nxf7 2410141K09Rik 2610042L04Rik B230110C06Rik
Esp38 Olfr1152 A530053G22Rik Sult2a3 Vmn1r167 Zfp936 Rbmxl2 Olfr539 Olfr986
Gm15455 Spic Esrrb Tcl1 Hist1h2ba Hhla1 Apobec3 Smim22 H2-Q10
Mymx Slc25a2 Olfr1497 Olfr1499 Ina Olfr339 Olfr354 Olfr1151 Olfr1298
Mir7003 Olfr1339 Olfr1338 Mir7229 Vmn2r23 Tas2r130 Gm31108 Mir290b Mir292b
Sult2a4 Psg29 Psg25 Nlrp9c Nphs1os Scgb2b18 Gm9268 Klk1 Olfr307
Olfr697 Olfr698 Olfr699 Olfr486 Olfr487 Olfr507 Olfr508 Olfr512 LOC105243090
Defb46 Defb11 Triml2 Zfp42 Olfr889 Olfr924 Dppa5a Fbxw15 Tdgf1
Lrrc2 Olfr807 Olfr401 Oog1 Akr1c19 Marcksl1-ps4 Tlr11 Vmn2r109 Esp5
Pcdhb3 Pcdhb13 Pcdhb14 Cyp2c66 Cyp2c68 Olfr367-ps Olfr1034 Olfr1045 Olfr1065
Olfr1090 Olfr1115 Olfr1234 Olfr48 Zfp345 LOC110008574 Mir302b Mir302c Mir302a
Mir302d Mir367 Mup6 Ugt2b38 Vmn1r12 Cacng7 Vmn2r62 Olfr635 Nlrp14
Olfr830 Olfr832 Olfr871 Mir363 Mir92-2 Mir19b-2 Mir20b Mir18b Mir6383 Foxr2
Gm6568 Sntg1 Defb44-ps Defb18 Defb41 Pih1d3 Prss40 F13b Cfhr1
Gm4788 Gpa33 Olfr418 Olfr427 Olfr231 Olfr420 Olfr414 B020014A21Rik 4930567K20Rik
C330004P14Rik Taar5 Calhm6 Lilr4b Mir6409 Nup37 Gm5176 Olfr784 Olfr806
4930554G24Rik Nlrp1c-ps Olfr382 Olfr385 Olfr384 Elobl Sfta3-ps Spanxn4 Tc2n
Gm29508 Speer6-ps1 Vmn1r193 Vmn1r208 Vmn1r211 Vmn1r212 Vmn1r213 Ctsr BC052688
2810049E08Rik Tmem267 3110070M22Rik Fezf2 Lrit1 Olfr724 Olfr725 Olfr731 Olfr733
Olfr736 Mir208a 4930444M15Rik 2610035F20Rik Capsl Dcstamp Abra Aard D730005E14Rik
Pla2g10os 4933404G15Rik Olfr165 Olfr166 Olfr170 Gm5416 Dppa4 Dppa2 Olfr196
Krtap13-1 Vmn2r124 Vmn2r91 Vmn2r92 Vmn2r94 Vmn2r95 Vmn2r96 Vmn2r97 Vmn2r98 Fpr-rs6
Vmn2r106 Vmn2r107 Vmn1r224 Vmn1r225 Vmn1r231 Vmn2r111 Vmn2r115 2410137M14Rik H2-M5
Olfr112 Olfr113 Olfr128 Olfr761 Olfr129 Olfr131 Esp24 Esp23 Esp15
Pgk2 Crisp3 Crisp1 Esp8 Glyatl3 2410021H03Rik Mir1195 4930480K15Rik 4930545E07Rik
Pcdhb8 LOC105246506 4930526L06Rik Olfr1463 Cyp2c53-ps Cyp2c67 Cyp2c40 Cyp2c69 Olfr338
Olfr340 Olfr351 Olfr353 Olfr356 Olfr357 Olfr358 Olfr365 Gm13580 Gm8541
Olfr993 Olfr995 Olfr998 Olfr1036 Olfr1038-ps Olfr1044 Olfr52 Olfr1051 Olfr1052
Olfr1055 Olfr1062 Olfr1082 Olfr1094 Olfr1097 Olfr1104 Olfr1122 Olfr1128 Olfr1129
Olfr1137 Olfr1140 Olfr152 Olfr1143 Olfr1181 Olfr1182 Olfr1188 Olfr1189 Olfr1196
Olfr1197 Olfr1198 Olfr1217 Olfr1231 Olfr1245 Olfr1251 Olfr1252 Olfr1256 Olfr1257
Pax6 Olfr1276 Olfr1277 Olfr1286 Olfr1290 Olfr1299 Olfr1302 Olfr1311 Olfr1312
Gjd2 Nkx2-4 Mybl2 Gtsf1l Gm8298 C130079G13Rik Aadacl2 Platr10 Lce1e
Tdpoz1 Tdpoz4 Chia1 Amy2a5 Olfr275 Olfr273 Mup4 Mup19 Mup20
Cyp2j8 B020004J07Rik Skint4 Skint3 Cyp4a10 Cyp4a31 Gm12887 Oog2 1700109H08Rik
4930425K10Rik Gnrhr Tmprss11g Ugt2b34 Ugt2a1 Csn1s2a Prr27 1700066N21Rik Smr3a
Smr2 Gm7714 1700041A01Rik Prol1 Naa11 Vmn2r9 Vmn2r10 Vmn2r11 Vmn2r12
Vmn2r14 Vmn2r17 Zfp932 Cyp3a16 Gm8579 Slc13a1 Tmem229a 1700074P13Rik Gm5409
Sval1 Olfr434 Vmn1r8 Vmn1r9 Vmn1r10 Vmn1r17 Vmn1r18 Vmn1r27 Vmn1r28
Vmn1r29 Vmn1r30 Atoh1 Vmn1r34 Mir6373 Gm19757 Olfr212 Gm10319 Clec4a4
Clec4b1 Clec4n Vmn2r22 Vmn2r25 5430401F13Rik Tas2r136 5530400C23Rik Gm5885 Mir290a
D7Ertd143e Nlrp12 Vmn1r58 Vmn1r59 Aurkc Vmn1r66 Vmn1r70 Nlrp4b Vmn1r71 Vmn1r74
Vmn1r75 Vmn1r76 Vmn1r77 Vmn1r78 Vmn1r79 Vmn1r80 Gm4224 Vmn1r82 Vmn1r84
Vmn2r54 Vmn2r55 Bsph2 Sult2a6 Psg-ps1 Ceacam14 Ceacam11 Ceacam13 Igfl3
Nlrp4e Nlrp5 Vmn1r171 Vmn1r172 Vmn1r175 Vmn1r178 Vmn1r179 Cyp2b9 Cyp2a22
Scgb2b20 Scgb2b23-ps Scgb2b24 A230077H06Rik Vmn2r59 Nell1os Olfr290 Vmn2r66 Vmn2r67
Vmn2r69 Vmn2r71 Vmn2r72 Vmn2r73 Vmn2r74 Vmn2r75 Vmn2r76 Vmn2r79 Olfr584
Olfr598 Olfr620 Olfr624 Olfr243 Olfr633 Olfr639 Olfr644 Olfr657 Olfr659
Gm1966 Olfr704 Olfr705 Olfr2 Olfr715b Olfr469 Olfr477 Olfr480 Olfr483
Olfr484 Olfr485 Olfr488 Olfr490 Olfr491 Olfr494 Olfr495 Olfr506 Olfr509
Olfr513 Acsm5 Defb6 Defb8 Triml1 Adam26a Gm5346 AY512931 1190028D05Rik
Sgo2b A330008L17Rik Alkbh8 Mmp12 Mmp20 Olfr828 Olfr834 Olfr835 Olfr836
Olfr837 Olfr843 Olfr857 Olfr868 Olfr872 Olfr873 Gm9513 Gm5615 Olfr888
Olfr891 Olfr899 Olfr147 Olfr901 Olfr912 Olfr913 Olfr923 Olfr926 Olfr944
Olfr951 Olfr960 Olfr150 Olfr967 Olfr969 Olfr970 Olfr982 1700055C04Rik Ooep
Trim43b Zic1 Zic4 Eras Gm2012 Kis2 Sox3 Ctag2 Mageb16
Nr0b1 Bex1 Platr21 Trap1a Alg13 Neurog3 4833422M21Rik Pcdhb9 Olfr1058
Olfr1107 Olfr29-ps1 Mir1963 EU599041 Tmed6 Zfp36l3 Gm614 Mgat4e Aire
Dnmt3l Spem2 Mir324 Hoxb13 Srp54c Tcl1b4 Tcstv1 Stfa1 Rnaset2a
Zfp955b 2410017I17Rik Gm8909 Gm6623 Frs3os Pcdhb5 Pcdhb10 Pcdhb19 Olfr1417
Olfr355 Olfr361 Olfr362 Cyct Olfr1057 Olfr141 Olfr1193 Olfr1313 1700017J07Rik
Gm3143 Gm38509 Cyp4b1-ps2 Rps15a-ps4 Cct8l1 Shh 4930548H24Rik Mir3965 Ankrd61
Mir141 Olfr1346 Apoc4 Kirrel2 Nphs1 Arhgap33os Scgb2b19 Olfr619 Olfr638
Olfr645 Olfr666 Olfr700 Sept1 C330021F23Rik Gm5907 Gm21119 AY761185 Defa21
Defa30 Defa17 Insl3 Olfr373 Mir7069 Mast1 Mir8110 Mir7073 Olfr853
Olfr859 Olfr27 Mir375 Fcgr3 Tstd1 Taar7e Sycp3 Olfr398 Gm11565
Btbd17 Nkx2-1 Tunar Ctsm Lrit2 1700109I08Rik Olfr741 Olfr742 Fitm1
Gm4371 Prm3 Mir3547 Cyp4f15 Olfr125 Olfr136 B430306N03Rik Mir7b Pcdhb12
Pcdhb17 Pcdhb18 Cyp26c1 Cyp2c39 Mir219b Olfr1076 Olfr1077-ps1 Olfr1102 Olfr1109
Olfr1110 Olfr1113 Olfr1148 Olfr1170 Olfr1248 Olfr1249 Zfp972 Sirpb1a Sirpb1b
Pou3f2 Cyp4x1os Ccdc24 Aadacl4 A930003O13Rik Asb10 Ucn Mir5098 Ugt2b36
Stx1a Dlx6 Gimap1 Vmn1r13 1700009C05Rik Tlx2 Gm15631 Tas2r129 Vmn2r53
Vmn1r89 Obox5 Nlrp9b Lypd5 Mag Gm5114 Vmn2r58 4933421I07Rik Mrgpra4
Snord64 Vmn2r77 Olfr594 Olfr600 Olfr606 Olfr675 Olfr693 Tmem205 A630095E13Rik
Olfr910 Fbxw13 Elp6 Prss45 Gm4984 Mir450-1 Mir450-2 Mir542 Tceal5
[ reached getOption("max.print") -- omitted 18 rows ]
$scale
[1] FALSE
$limits
[1] -2 2
$color
[1] "#352A86" "#342B89" "#342D8C" "#342E8F" "#343092" "#343196" "#343399" "#34349C" "#34369F" "#3437A3" "#3439A6"
[12] "#343AA9" "#343CAC" "#313EB0" "#2D41B4" "#2944B8" "#2547BC" "#214AC0" "#1D4DC4" "#1950C8" "#1553CC" "#1156D0"
[23] "#0D59D4" "#095CD8" "#055FDC" "#0262DF" "#0365DE" "#0569DD" "#066CDC" "#076FDB" "#0972DA" "#0A75D8" "#0B78D7"
[34] "#0D7CD6" "#0E7FD5" "#1082D4" "#1185D3" "#1288D2" "#148CCE" "#168FCA" "#1993C7" "#1B97C3" "#1D9BBF" "#1F9EBB"
[45] "#21A2B7" "#23A6B4" "#25A9B0" "#27ADAC" "#29B1A8" "#2BB5A4" "#31B7A0" "#3BB79C" "#45B897" "#4EB892" "#58B98E"
[56] "#62BA89" "#6CBA85" "#75BB80" "#7FBB7B" "#89BC77" "#92BC72" "#9CBD6E" "#A5BD69" "#ACBD66" "#B3BD63" "#B9BC60"
[67] "#C0BC5C" "#C7BC59" "#CEBC56" "#D4BB53" "#DBBB50" "#E2BB4D" "#E8BA4A" "#EFBA46" "#F6BA43" "#F7BB41" "#F7BE3E"
[78] "#F7C13B" "#F7C339" "#F7C636" "#F7C834" "#F6CB31" "#F6CE2E" "#F6D02C" "#F6D329" "#F6D527" "#F6D824" "#F6DA22"
[89] "#F6DD20" "#F6E01E" "#F6E21C" "#F6E51B" "#F6E719" "#F7EA17" "#F7ED15" "#F7EF14" "#F7F212" "#F7F410" "#F7F70E"
[100] "#F8FA0D"
$clusterCols
[1] FALSE
$clusterRows
[1] FALSE
$labelRows
[1] TRUE
$labelCols
[1] FALSE
$customColLabel
integer(0)
$showRowDendrogram
[1] TRUE
$draw
[1] FALSE
$name
[1] "Column Z-Scores\n2432 features\nGeneScoreMatrix"`It says FALSE next to "draw" so maybe that's where the problem is with generating the heatmap
rcorces
commented
3 years ago can you instead show what str(heatmapGS) shows?
spietrzak
commented
3 years ago Here is that output:
> str(heatmapGS) List of 12 $ mat : num [1:18, 1:2432] 1.587 0.545 -0.122 -0.566 -0.682 ... ..- attr(*, "dimnames")=List of 2 .. ..$ : chr [1:18] "C2" "C4" "C18" "C15" ... .. ..$ : chr [1:2432] "Serpinb6b" "Ptk2b" "Serinc3" "Ccl11" ... $ scale : logi FALSE $ limits : num [1:2] -2 2 $ color : chr [1:100] "#352A86" "#342B89" "#342D8C" "#342E8F" ... $ clusterCols : logi FALSE $ clusterRows : logi FALSE $ labelRows : logi TRUE $ labelCols : logi FALSE $ customColLabel : int(0) $ showRowDendrogram: logi TRUE $ draw : logi FALSE $ name : chr "Column Z-Scores\n2432 features\nGeneScoreMatrix"
rcorces
commented
3 years ago ok. thats definitely not what should be returned but I havent figured out why you're getting that. it should be an object of class Heatmap. Perhaps the cutoffs you have set are too stringent and nothing passes those filters? Can you try making those more permissive?
> str(heatmapGS)
Formal class 'Heatmap' [package "ComplexHeatmap"] with 31 slots
..@ name : chr "Column Z-Scores\n2670 features\nGeneScoreMatrix"
..@ matrix : num [1:12, 1:2670] 0.369 0.383 0.565 0.713 0.164 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:12] "C1" "C2" "C3" "C4" ...
.. .. ..$ : chr [1:2670] "LINC00323" "CRHBP" "IGFBPL1" "KRT85" ...
..@ matrix_param :List of 11
TRUNCATED HERE FOR VISIBILITYSorry that doesn't look very nice. Here is a screenshot (I'm still trying to figure out how exactly to copy code or lines from R into here)
rcorces
commented
3 years ago To copy blocks of code, use the block syntax for markdown which requires you to put three backticks before and after the code block "```" https://www.markdownguide.org/extended-syntax/
spietrzak
commented
3 years ago I don't think that my FDR and FC change cutoffs are too stringent, because I was able to output a table of the marker genes at this cutoff and there were a little over 3000 rows of marker genes. I think it is just a problem with drawing the heatmap
rcorces
commented
3 years ago Can you try two things:
1) set labelMarkers to NULL in your call to plotMarkerHeatmap() and see if it still causes a problem
2) upload a logfile from plotMarkerHeatmap()
spietrzak
commented
3 years ago After setting labelMarkers to NULL, the error no longer appeared and I was able to generate a heatmap. Thanks for your help. Still unsure as to why it wasn't working since I had done that previously with other data and I haven't updated ArchR or any other packages.
rcorces
commented
3 years ago My suspicion is that one of the markers in your labelMarkers object is not found in the gene names of your markerGS object and this is somehow corrupting the Heatmap object. Presumably in this codeblock. I'll continue to look into it:
https://github.com/GreenleafLab/ArchR/blob/968e4421ce7187a8ac7ea1cf6077412126876d5f/R/ArchRHeatmap.R#L176
rcorces
commented
3 years ago I'm not able to recapitulate this on my end and have not been able to figure out the underlying cause to this issue. Could perhaps be some incompatibility of different versions of ComplexHeatmap. If any one else runs into this and has bandwidth to help figure out the underlying cause, let me know.
Kaivalyamolugu
commented
3 years ago Hello @rcorces , I just wanted to add that I was having the same issue which got resolved by setting LabelMarkers = NULL. Also, does this mean that we can no longer plot the marker genes set by the user on the heatmap? I am no longer able to visualize marker genes on an embedding (7.4). I get NULL as output if I try to visualize a marker gene of my choice. I used NANOG in this case.
Code: markerList <- getMarkers(markersGS, cutOff = "FDR <= 0.01 & Log2FC >= 1.25") markerGenes <- c("NANOG") p <- plotEmbedding( ArchRProj = proj2, colorBy = "GeneScoreMatrix", name = markerGenes, embedding = "UMAP", quantCut = c(0.01, 0.95), imputeWeights = NULL )
p$Nanog
Output: NULL
rcorces
commented
3 years ago @Kaivalyamolugu - I dont think those are related. Is "NANOG" in your GeneScoreMatrix?
Kaivalyamolugu
commented
3 years ago @rcorces Is there a way I could check that? I'm a bit confused because I was analyzing the same dataset, and was able to plot browser tracks and other maps for the genes I specified (including NANOG) in markerGenes two months ago. I'm not sure what changed. Please let me know if you'd prefer that I can create a new issue detailing the problem. Thanks, Kaivalya
rcorces
commented
3 years ago @Kaivalyamolugu - Sorry, I should have read your post more clearly. Your problem is that you are only providing one gene ("NANOG") so the return is a single plot, not multiple. So you access the plot using p not p$NANOG
Kaivalyamolugu
commented
3 years ago @rcorces That worked. Thank you so much!
rcorces
commented
2 years ago I'm closing this since I'm not able to recapitulate the error and this is rather old now. Feel free to comment more below if you run into this same problem again.
I have begun an analysis in ArchR and tried to generate the marker gene heatmap using the following command:
`heatmapGS <- markerHeatmap( seMarker = markersGS, cutOff = "FDR <= 0.01 & Log2FC >= 1.25", labelMarkers = markerGenes, transpose = TRUE )
ComplexHeatmap::draw(heatmapGS, heatmap_legend_side = "bot", annotation_legend_side = "bot")`
However, I am getting the following error:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘draw’ for signature ‘"list"’I am not entirely sure what this error is saying. I have used ArchR to perform analysis on several samples before, but this is the first time I am running into this issue at this step. Any information on how to resolve this would be greatly appreciated.