Different result of "Visualize average top pairs genes expression for training data"

[hyjforesight]

Hello Yuqi, When I am running the "Visualize average top pairs genes expression for training data" part, there comes a big list of missing genes and a Warning message: In brewer.pal(n = 12, name = "Spectral") : n too large, allowed maximum for palette Spectral is 11 Returning the palette you asked for with that many colors

The result is like this, not like what you show in the tutorial.

Could you please tell me how to fix this issue? Thanks! Best, YJ

[yuqiyuqitan]

Hi YJ,

I don't have enough information about what you did to figure out what went wrong. Can you elaborate?

[hyjforesight]

Hello Yuqi, Please check the following coding. Thanks!

stPark = utils_loadObject("sampTab_Park_MouseKidney_062118.rda")

expPark = utils_loadObject("expMatrix_Park_MouseKidney_Oct_12_2018.rda") dim(expPark) [1] 16272 43745 [1] 16272 43745 Error: unexpected '[' in "["

genesPark = rownames(expPark)

rm(expPark) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 2069336 110.6 4191592 223.9 2572041 137.4 Vcells 4421116 33.8 71591799 546.3 72832775 555.7

expTMraw = utils_loadObject("expMatrix_TM_Raw_Oct_12_2018.rda") dim(expTMraw) [1] 23433 24936 [1] 23433 24936 Error: unexpected '[' in "["

stTM = utils_loadObject("sampTab_TM_053018.rda") dim(stTM) [1] 24936 17 [1] 24936 17 Error: unexpected '[' in "["

stTM<-droplevels(stTM)

commonGenes = intersect(rownames(expTMraw), genesPark) length(commonGenes) [1] 13831 [1] 13831 Error: unexpected '[' in "["

expTMraw = expTMraw[commonGenes,]

set.seed(100) #can be any random seed number stList = splitCommon(sampTab=stTM, ncells=100, dLevel="newAnn") alveolar macrophage : Category alveolar macrophage has 62 samples. Note this category has a samller number than ncells. 62 B cell : 3134 bladder urothelial cell : 759 bladder_mesenchymal : 859 cardiac muscle cell : Category cardiac muscle cell has 60 samples. Note this category has a samller number than ncells. 60 cardiac_fibroblast : 222 chondrocyte-like : 165 endocardial cell : Category endocardial cell has 52 samples. Note this category has a samller number than ncells. 52 endothelial cell : 1890 erythroblast : 152 erythrocyte : Category erythrocyte has 74 samples. Note this category has a samller number than ncells. 74 granulocyte : 520 hematopoietic precursor cell : 117 hepatocyte : 882 keratinocyte : 1203 kidney capillary endothelial cell : 117 kidney proximal straight tubule epithelial cell : 618 kidney_duct_epithelial : 355 late pro-B cell : 141 limb_mesenchymal : 540 luminal epithelial cell of mammary gland : 137 lung_mammary_stromal : 2072 macrophage : 1340 mammary_basal_cell : 115 monocyte : 370 natural killer cell : 600 neuroendocrine cell : 282 skeletal muscle satellite cell : 190 T cell : 1823 tongue_basal_cell : 1726 trachea_epithelial : 434 trachea_mesenchymal : 3925 stTrain = stList[[1]] expTrain = expTMraw[,rownames(stTrain)]

system.time(class_info<-scn_train(stTrain = stTrain, expTrain = expTrain, nTopGenes = 10, nRand = 70, nTrees = 1000, nTopGenePairs = 25, dLevel = "newAnn", colName_samp = "cell")) Sample table has been prepared Expression data has been normalized Finding classification genes Done testing There are 484 classification genes Finding top pairs nPairs = 190 for alveolar macrophage nPairs = 190 for B cell nPairs = 190 for bladder urothelial cell nPairs = 190 for bladder_mesenchymal nPairs = 190 for cardiac muscle cell nPairs = 190 for cardiac_fibroblast nPairs = 190 for chondrocyte-like nPairs = 190 for endocardial cell nPairs = 190 for endothelial cell nPairs = 190 for erythroblast nPairs = 190 for erythrocyte nPairs = 190 for granulocyte nPairs = 190 for hematopoietic precursor cell nPairs = 190 for hepatocyte nPairs = 190 for keratinocyte nPairs = 190 for kidney capillary endothelial cell nPairs = 190 for kidney proximal straight tubule epithelial cell nPairs = 190 for kidney_duct_epithelial nPairs = 190 for late pro-B cell nPairs = 190 for limb_mesenchymal nPairs = 190 for luminal epithelial cell of mammary gland nPairs = 190 for lung_mammary_stromal nPairs = 190 for macrophage nPairs = 190 for mammary_basal_cell nPairs = 190 for monocyte nPairs = 190 for natural killer cell nPairs = 190 for neuroendocrine cell nPairs = 190 for skeletal muscle satellite cell nPairs = 190 for T cell nPairs = 190 for tongue_basal_cell nPairs = 190 for trachea_epithelial nPairs = 190 for trachea_mesenchymal There are 797 top gene pairs Finished pair transforming the data Number of missing genes 0 All Done user system elapsed 616.27 22.44 643.94

#validate data stTestList = splitCommon(sampTab=stList[[2]], ncells=100, dLevel="newAnn") #normalize validation data so that the assessment is as fair as possible alveolar macrophage : Category alveolar macrophage has 3 samples. Note this category has a samller number than ncells. 3 B cell : 3034 bladder urothelial cell : 659 bladder_mesenchymal : 759 cardiac muscle cell : Category cardiac muscle cell has 3 samples. Note this category has a samller number than ncells. 3 cardiac_fibroblast : 122 chondrocyte-like : Category chondrocyte-like has 65 samples. Note this category has a samller number than ncells. 65 endocardial cell : Category endocardial cell has 3 samples. Note this category has a samller number than ncells. 3 endothelial cell : 1790 erythroblast : Category erythroblast has 52 samples. Note this category has a samller number than ncells. 52 erythrocyte : Category erythrocyte has 3 samples. Note this category has a samller number than ncells. 3 granulocyte : 420 hematopoietic precursor cell : Category hematopoietic precursor cell has 17 samples. Note this category has a samller number than ncells. 17 hepatocyte : 782 keratinocyte : 1103 kidney capillary endothelial cell : Category kidney capillary endothelial cell has 17 samples. Note this category has a samller number than ncells. 17 kidney proximal straight tubule epithelial cell : 518 kidney_duct_epithelial : 255 late pro-B cell : Category late pro-B cell has 41 samples. Note this category has a samller number than ncells. 41 limb_mesenchymal : 440 luminal epithelial cell of mammary gland : Category luminal epithelial cell of mammary gland has 37 samples. Note this category has a samller number than ncells. 37 lung_mammary_stromal : 1972 macrophage : 1240 mammary_basal_cell : Category mammary_basal_cell has 15 samples. Note this category has a samller number than ncells. 15 monocyte : 270 natural killer cell : 500 neuroendocrine cell : 182 skeletal muscle satellite cell : Category skeletal muscle satellite cell has 90 samples. Note this category has a samller number than ncells. 90 T cell : 1723 tongue_basal_cell : 1626 trachea_epithelial : 334 trachea_mesenchymal : 3825 stTest = stTestList[[1]] expTest = expTMraw[commonGenes,rownames(stTest)]

#predict classRes_val_all = scn_predict(cnProc=class_info[['cnProc']], expDat=expTest, nrand = 50) Loaded in the cnProc All Done

tm_heldoutassessment = assess_comm(ct_scores = classRes_val_all, stTrain = stTrain, stQuery = stTest, dLevelSID = "cell", classTrain = "newAnn", classQuery = "newAnn", nRand = 50)

plot_PRs(tm_heldoutassessment)

plot_metrics(tm_heldoutassessment)

#Create a name vector label used later in classification heatmap where the values are cell types/ clusters and names are the sample names

nrand = 50 sla = as.vector(stTest$newAnn) names(sla) = as.vector(stTest$cell) slaRand = rep("rand", nrand) names(slaRand) = paste("rand_", 1:nrand, sep='') sla = append(sla, slaRand) #include in the random cells profile created

sc_hmClass(classMat = classRes_val_all,grps = sla, max=300, isBig=TRUE)

plot_attr(classRes=classRes_val_all, sampTab=stTest, nrand=nrand, dLevel="newAnn", sid="cell") Warning message: In depth(path) : reached elapsed time limit

gpTab = compareGenePairs(query_exp = expTest, training_exp = expTrain, training_st = stTrain, classCol = "newAnn", sampleCol = "cell", RF_classifier = class_info$cnProc$classifier, numPairs = 20, trainingOnly= TRUE)

train = findAvgLabel(gpTab = gpTab, stTrain = stTrain, dLevel = "newAnn")

hm_gpa_sel(gpTab, genes = class_info$cnProc$xpairs, grps = train, maxPerGrp = 50) Missing genes: Ear2_Ifitm3,Ear2_Ubb,Abcg1_Ubc,Ear2_Ifitm2,Abcg1_Ubb,Abcg1_Nfkbia,Mpeg1_Ifitm3,Mpeg1_Ubb,Il18_Nfkbia,Mpeg1_Ifitm2,Sirpa_Ifitm2,Il18_Ifitm3,Il1rn_Nfkbia,Nceh1_Ubc,Il18_Jun,Klhdc4_Ubc,Il1rn_S100a6,Il1rn_Jun,Sirpa_Jun,Sirpa_Xist,Nceh1_Xist,Pla2g15_Xist,Ccl6_S100a6,Nceh1_Cd63,Pla2g15_Cd63,H2-Ob_Txn1,Cd79b_Txn1,Cd79a_Txn1,H2-Eb1_Itm2b,H2-Aa_Itm2b,H2-Ob_Ifitm3,H2-Ob_Ifitm2,H2-Oa_S100a6,H2-Oa_Ifitm3,H2-Oa_Anxa2,Cd79a_S100a6,Cd79b_Ifitm2,Cd79b_Ifitm3,H2-Eb1_Ifitm2,H2-Eb1_Anxa2,H2-Aa_Dstn,H2-Aa_S100a6,Cd37_Anxa2,Cd37_Dstn,Cd19_Dstn,H2-Ab1_Cd63,Cd19_Cd63,H2-Ab1_Cd9,Cd19_Cd9,Upk1a_Lgals1,Upk1a_Vim,Ivl_Nfkbia,Ivl_Vim,Ivl_Aldh2,Upk1b_Ifitm3,Foxq1_Hspa8,Upk1b_Aldh2,Upk1b_Emp3,Akr1b8_Ifitm3,Akr1b8_S100a10,Sprr1a_Hspa8,Foxq1_B2m,Krt23_Nfkbia,Krt23_S100a10,Krt23_Ifitm3,Akr1b8_Nfkbia,2200002D01Rik_S100a10,Krt7_Hspa8,2200002D01Rik_B2m,Foxq1_Lgals1,Sprr1a_B2m,Sprr1a_Lgals1,Krt7_Xist,Mmp23_Xist,Tcf21_Xist,Bmp4_Xist,Serpina3n_Chchd10,Serpina3n_Ucp2,Serpina3n_Coro1a,Mmp23_Ucp2,Bmp4_Chchd10,Bmp4_Srgn,Mmp23_Cd52,Col12a1_Cd24a,Col12a1_Srgn,Col12a1_Cd52,Thbs2_Srgn,Thbs2_Cd24a,Thbs2_Rac2,Htra1_Cd24a,Col1a2_Col3a1,Htra1_Coro1a,Htra1_Laptm5,Tnni3_Rps19,Tnni3_Ftl1,Tnni3_Actb,Smpx_Actb,Tnnt2_Rps19,Tnnt2_Actb,Tnnc1_Ppia,Tnnc1_H3f3b,Cox8b_Actg1,Pln_Myl6,Cox6a2_Rps19,Tnnt2_Ptma,Tnnc1_Actg1,Cox8b_Ptma,Cox8b_H3f3b,Csrp3_Ppia,Smpx_Myl6,Cox6a2_Ftl1,Cox6a2_Ppia,Smpx_Actg1,Csrp3_Ftl1,Pln_H3f3b,Csrp3_Myl6,Pln_Ptma,Ttn_Cfl1,Tcf21_Fosb,Matn2_Fosb,Cygb_Fosb,Col15a1_Btg1,Tcf21_Ier5,Matn2_Lgals3,Matn2_Ier5,Col15a1_Ier5,Htra3_Btg1,Tcf21_Btg1,Scn7a_Atp1a1,Scn7a_Lgals3,Scn7a_Spint2,Htra3_Slc25a5,Col15a1_Slc25a5,Cygb_Slc25a5,Cygb_Atp1a1,Htra3_Cox5a,Cfh_Cox5a,Ccdc80_Cox5a,Cfh_Lgals3,Cfh_Ucp2,Ccdc80_Atp1a1,Ccdc80_Ucp2,Fbln1_Spint2,Fmod_Uba52,Cilp2_Ndufa4,Cilp2_Ndufb7,Thbs4_Cox6b1,Thbs4_Ndufa4,Cilp2_Atp5g2,Serpinf1_Uba52,Fmod_Cox6b1,Fmod_Atp5g2,Angptl7_H2afj,Angptl7_Uqcrfs1,Comp_Ndufa4,Angptl7_Ucp2,Comp_Cox6b1,Comp_Atp5g2,Fbln7_Uqcrq,Col12a1_Ndufb7,Col12a1_H2afj,Fbln7_Ucp2,Fbln7_H2afj,Abi3bp_Uqcrq,Timp1_Uqcrq,Abi3bp_Ndufb7,Npr3_Jund,Npr3_Junb,Npr3_S100a6,Hmcn1_S100a6,Foxc1_Mt1,Mmrn2_Jund,Hmcn1_Jund,Hmcn1_Mt1,Mmrn2_Junb,Foxc1_Junb,Bace2_S100a6,Mmrn2_Fos,Bace2_Atf4,Bace2_Mt1,Foxc1_Fos,Ptgs1_Fos,Ptgs1_Ier3,Ptgs1_Atf4,Cgnl1_Atf4,Cgnl1_Mt2,Cgnl1_Fosb,Sdpr_Fosb,Sdpr_Ier3,Sdpr_Mt2,Eng_Ier3,Gpihbp1_Rpl12,Gpihbp1_Ndufa13,Gpihbp1_Atp5e,Rnd1_Rps28,Cdh5_Ndufa13,Cdh5_Cox8a,Ly6c1_Rps9,Ly6c1_Rpsa,Cdh5_Prdx5,Ly6c1_Rps28,Rnd1_Rpl12,Apold1_Ndufa13,Apold1_Rpl12,Rnd1_Rps9,Esam_Cox8a,Esam_Atp5e,Apold1_Prdx5,Fabp4_Rps9,Flt1_Prdx5,Fabp4_Rps28,Fabp4_Cox8a,Flt1_H2afj,Rasip1_H2afj,Ptprb_H2afj,Flt1_Atp5e,Slc4a1_Nme2,Alas2_Hspa8,Hba-a2_Ybx1,Alas2_Rps21,Hba-a2_Nme2,Alas2_Ppia,Hba-a2_Hsp90ab1,Snca_Ybx1,Snca_Hsp90ab1,Slc4a1_Ybx1,Snca_Nme2,Slc4a1_Hspa8,Hba-a1_Hspa8,Hba-a1_Actg1,Hba-a1_Hsp90ab1,Ube2l6_Actg1,Car2_Rpl36,Car2_Ppia,Fech_Ppia,Fech_Rpl36,Ube2l6_Rpl38,Fech_Rpl38,Car2_Rpl38,Ube2l6_Rps21,Slc25a37_Actg1,Folr2_Cd9,Folr2_Crip2,Folr2_S100a16,C1qb_Crip2,C1qc_Crip2,C1qc_Cd9,C1qc_Nedd4,C1qb_Nedd4,C1qb_Serpinh1,C1qa_Nedd4,C1qa_Cd9,C1qa_Serpinh1,Csf1r_Anxa1,Pf4_Anxa1,Aif1_Anxa1,Pf4_Csrp1,Aif1_Csrp1,Pf4_Tsc22d1,Hpgd_S100a16,Csf1r_Csrp1,Hpgd_Hspb1,Aif1_Tsc22d1,Csf1r_Tsc22d1,Hpgd_Nfib,Fcgr3_S100a16,Cd177_Nme2,Cd177_Hsp90ab1,Ngp_Rpl41,Trem3_Nme2,Ifitm6_Rpl10,Pglyrp1_Rpl41,Ifitm6_Rplp1,Ifitm6_Rpl35,Ltf_Rpl41,Trem3_Hsp90ab1,Pglyrp1_Eef1a1,Pglyrp1_Rpl10,Cd177_Rpl14,Ltf_Rplp1,Ltf_Rpl35,Ngp_Rpl10,Ngp_Rplp1,Camp_Eef1a1,Camp_Rpl35,Camp_Rps2,Trem3_Rpl14,Lcn2_Eef1a1,Lcn2_Rps2,S100a9_Rps2,S100a9_Rpl14,Prtn3_S100a6,Prtn3_Ubc,Myb_Gsn,Prtn3_Fth1,Myb_Id3,Cmtm7_Ubc,Rgs18_Gsn,Plac8_Fth1,Atp8b4_S100a6,Ramp1_Ubc,Ramp1_Gsn,Phgdh_Lmna,Ramp1_S100a6,Atp8b4_Ptms,Atp8b4_Ahnak,Rgs18_Ptms,Phgdh_Ptms,Phgdh_Id3,Rgs18_Id3,BC035044_Ahnak,Clec12a_Ahnak,BC035044_Crip2,BC035044_Lmna,Clec12a_Crip2,Serpina1c_Rpl23a,Serpina1c_Rps9,Serpina1c_Rpl21,Serpina1b_Rpl23a,Serpina1b_Rps9,Serpina1b_Tmsb4x,Apoa1_Rpl23a,Apoa1_Rps9,Apoa1_Rpl21,Apoa2_Rps23,Serpina1a_Rpl21,Serpina1a_Rpl9,Serpina1a_Rpl13,Apoc3_Rpl9,Apoc3_Rplp2,Apoc3_Rpl13,Alb_Rplp2,Apoa2_Rpl9,Apoa2_Rplp2,Alb_Actg1,Apoc4_Tmsb4x,Alb_Rpl13,Serpina1d_Tmsb4x,Apoc4_Actg1,Serpina1d_Actg1,Them5_Fth1,S100a14_Fth1,Calml3_Fth1,Calml3_Gpx4,Ovol1_Gpx4,Rab25_Gpx4,Aldh3b2_Arpc1b,Sbsn_Ftl1,Them5_Ftl1,Rab25_Ftl1,Tgm1_Arpc1b,Tgm1_Cyba,Tgm1_B2m,Calml3_B2m,Them5_Arpc1b,Aldh3b2_B2m,Ovol1_H2-K1,Aldh3b2_Serinc3,Ovol1_Serinc3,Sbsn_H2-K1,S100a14_H2-K1,Sbsn_Vim,Lgals7_Xist,S100a14_Serinc3,Lgals7_Cyba,Meis2_Gsn,Meis2_Cd63,Clec14a_Gsn,Slc9a3r2_Gsn,Plscr2_Cd63,Clec14a_Cd63,Meis2_Mt1,Emcn_Rplp0,Podxl_Mt1,Clec14a_Cebpb,Slc9a3r2_Rpsa,Slc9a3r2_Rplp0,Ptprb_Mt1,Ptprb_Mt2,Emcn_Rpsa,Emcn_Rps27a,Ptprb_Lgals1,Podxl_Mt2,Kdr_Lgals1,Podxl_Sdc4,Egfl7_Lgals1,Kdr_Cebpb,Egfl7_Rpsa,Kdr_Sdc4,Plscr2_Sdc4,Tmem27_Rps6,Slc34a1_H3f3b,Slc34a1_Rpl9,Tmem27_Eif1,Tmem27_Rpl9,Slc34a1_Rps6,Miox_Eif1,Miox_Rpl9,Acsm2_Tmsb4x,Acsm2_H3f3b,Miox_Rps4x,Acsm2_H2-D1,Akr1c21_Rps6,Akr1c21_Tmsb4x,Slc22a8_Tmsb10,Slc22a8_Tmsb4x,Akr1c21_H3f3b,Lrp2_Tmsb10,Fut9_H2-D1,Fut9_Myl12a,Lrp2_Myl12a,Lrp2_H2-D1,Slc22a8_Myl12a,Fut9_Tmsb10,Pdzk1_Rps4x,Kcnj1_Arpc1b,Kng2_B2m,Egf_B2m,Kcnj1_B2m,Ppp1r1a_Rpl4,Egf_Rps16,Egf_Rpl4,Ppp1r1a_Rps6,Wfdc15b_Rps16,Wfdc15b_Rpl4,Wfdc15b_Rpl10,Ppp1r1a_Tmsb4x,Kcnj1_Tmsb4x,Umod_Rps16,Umod_Rpl10,Umod_Rps19,Tmem213_Arpc1b,Sostdc1_Tmsb4x,Clcnkb_Arpc1b,Klk1_Rps6,Klk1_Rpl18a,Klk1_Rps19,Kng2_Rps6,Sostdc1_Rpl18a,Kng2_Rps27a,Pou2af1_Rabac1,Lrmp_Aldoa,Vpreb3_Aldoa,Lrmp_Itm2b,Lmnb1_Itm2b,Pafah1b3_Aldoa,Vpreb3_Rabac1,Lrmp_Rabac1,Pou2af1_Anxa5,Uhrf1_Ifitm3,Pou2af1_Laptm4a,Cenpm_Anxa2,Uhrf1_Anxa2,Cenpm_Ifitm3,Pafah1b3_Laptm4a,Pafah1b3_Anxa2,Top2a_Ifitm3,Cenpm_Anxa5,Uhrf1_Anxa5,Top2a_S100a6,Ezh2_Laptm4a,2810417H13Rik_S100a6,Top2a_Cd63,Ezh2_S100a6,Ifi205_Slc25a5,Ifi205_Ucp2,Ifi205_Cox6b1,Mnda_Arhgdib,Mnda_Ucp2,Mnda_Taldo1,Clec3b_Uqcr11,Clec3b_Cox6b1,Clec3b_Ndufa4,Gfpt2_Cox6b1,Col5a3_Uqcr11,Nid1_Ndufa4,Col5a3_Slc25a5,Itm2a_Uqcr11,Itm2a_Ndufa4,Itm2a_Slc25a5,Col5a3_Taldo1,Gfpt2_Spint2,Fbln2_Spint2,Tnxb_Taldo1,Gfpt2_Cd24a,Tnxb_Spint2,Fbln2_Ucp2,Tnxb_Arhgdib,Fbln2_Cd24a,Cldn7_Gstm1,Cldn3_Gstm1,Cldn3_Mgp,Krt19_Gstm1,Cldn3_Id3,Cldn7_Btg2,Krt19_Lgals1,Ptn_Id3,Krt19_Mgp,Ptn_Sparc,Cldn7_Mgp,Ptn_Aldh2,St14_Btg2,Prlr_Aldh2,Krt18_Aldh2,Epcam_Btg2,St14_Id3,St14_Sparc,Krt18_Lgals1,Krt18_Sparc,Krt8_Lgals1,Epcam_Cd47,Sod3_Tpt1,Sod3_Hspa8,Inmt_Eef1a1,Inmt_Uba52,Ppp1r14a_Hspa8,Sod3_Hsp90ab1,Pcolce2_Hspa8,Ppp1r14a_Hsp90ab1,Fhl1_Hsp90ab1,Inmt_Tpt1,Ppp1r14a_Cox4i1,Pcolce2_Fau,Pcolce2_Tpt1,Npnt_Gapdh,Lrp4_Gapdh,Fhl1_Uba52,Limch1_Cox4i1,Lrp4_Pabpc1,Limch1_Gapdh,Fhl1_Cox4i1,Npnt_Pabpc1,Npnt_Cox5a,Tbx2_Pabpc1,Lrp4_Cox5a,Limch1_Cox5a,Il1b_Dstn,Il1b_Jun,Il1b_Pebp1,Bcl2a1d_Dstn,H2-DMb1_Pebp1,Cd83_Pebp1,Aif1_Mgst1,Cd83_Jun,Bcl2a1d_Mgst1,H2-DMb1_Dstn,Cd83_Tubb4b,Aif1_Tubb4b,Bcl2a1b_Mgst1,Bcl2a1b_Tubb4b,Bcl2a1d_Jun,Aif1_Gstm1,Bcl2a1b_Nedd4,H2-DMb1_Gstm1,H2-Aa_Crip2,H2-Aa_Nedd4,H2-Aa_S100a16,H2-Eb1_Nedd4,H2-Eb1_S100a16,H2-Eb1_Serpinh1,H2-Ab1_Crip2,Fst_Crip1,Tpm2_Itm2b,Tagln_Crip1,Fst_Cst3,Tagln_Cst3,Fst_Dusp1,Tpm2_Serf2,Acta2_Itm2b,Acta2_Crip1,Tagln_Itm2b,Acta2_Cst3,Cda_Ndufv3,Arl4c_Sh3bgrl3,Fermt1_Btg2,Palld_Btg2,Fermt1_Ndufv3,Fermt1_Fos,Slpi_Sh3bgrl3,Palld_Dusp1,Palld_Zfp36,Tpm2_Fos,Arl4c_Serf2,Cxcl14_Serf2,Cxcl14_Fos,Cda_Dusp1,Ccr2_Mt1,Ccr2_Cd9,Ccr2_Zfp36l1,Ms4a6c_Mt1,Pld4_Cd81,Ms4a6c_Cd81,F13a1_Mt1,F13a1_Cd63,F13a1_Cd81,Ms4a6c_Cd63,Ms4a4c_Zfp36l1,Ms4a4c_Hmgn1,Tifab_Hmgn1,Ms4a4c_Sdc4,Pld4_Zfp36l1,Pld4_Cd63,Tifab_Cd9,Tifab_Sdc4,Ly86_Hmgn1,Ccl9_Sdc4,Ccl9_Cd9,Ccl9_Lmna,Ly86_Lmna,Ly86_Igfbp7,Lyz1_Lmna,Ncr1_App,Ncr1_Dstn,Ncr1_Ifitm3,Klrb1c_Mt1,Klrb1c_Gpx1,Klrb1c_App,Gzma_Gpx1,Klre1_Mt1,Ccl5_Fth1,Klre1_Ctsb,Gzma_Ctsb,Klre1_App,Klrk1_Gpx1,Klrk1_Ctsb,Klrk1_Ifitm3,Nkg7_Fth1,Gzmb_Mt1,Gzmb_Cd81,Gzmb_Ifitm2,Klrd1_Ifitm3,Klrd1_Ifitm2,Klrd1_Dstn,Ccl5_Dstn,Ccl5_Ifitm2,Rgs5_Rps28,Rgs5_Rps21,Myl9_Rpl39,Rgs5_Eef1b2,Plp1_Xist,Plp1_Eef1b2,Mpz_Rps28,Plp1_Rps28,Mpz_Rps21,Mpz_Eef1b2,Gm13889_Rpl38,Myl9_Rps21,Myl9_Rpl38,Sncg_Ly6e,Gm13889_Rpl39,Mbp_Uba52,Mbp_Rps29,Mbp_Rpl38,Gm13889_Rps29,Mustn1_Rpl39,Sncg_Xist,Mustn1_Rps10,Cryab_Rps29,Mustn1_Ly6e,Sncg_Rps10,Asb5_Ndufa3,Asb5_Gpx1,Crlf1_Clic1,Des_Ndufa3,Crlf1_Itm2b,Des_Ndufa4,Des_Gpx1,Meg3_Itm2b,Arl4d_Ndufa4,Meg3_Serf2,Crlf1_Gpx1,Akap2_Itm2b,Pdlim4_Clic1,Ncam1_Ndufa3,Chrnb1_Clic1,Ncam1_Ostf1,Chrnb1_Ly6e,Arl4d_Ly6e,Cd82_Ndufa4,Pdlim4_Ly6e,Chrnb1_Sh3bgrl3,Cd82_Serf2,Cd82_Sh3bgrl3,Arl4d_H2afj,Lat_Rps27l,Lat_Dstn,Lat_Aldh2,Lck_Rps27l,Ms4a6b_Ifitm3,Ms4a6b_Ifitm2,Ms4a6b_Cst3,Lck_Cst3,Lck_Aldh2,Ms4a4b_Rps27l,Ms4a4b_Aldh2,Ms4a4b_Ifitm3,Satb1_Ifitm2,Ltb_Dstn,Satb1_Ifitm3,Ltb_Cd81,Satb1_Cd81,Ltb_Cd63,Cd2_Cd81,Limd2_Itm2b,Gimap3_Cd63,Gimap3_Laptm4a,Wnt10a_Xist,Wnt10a_H2-K1,Wnt10a_B2m,Them5_Vim,Them5_Sepp1,S100a14_B2m,S100a14_H2-D1,Moxd1_Lgals1,Moxd1_B2m,Lgals7_H2-D1,Plek2_Serinc3,Moxd1_Vim,Lgals7_H2-K1,Plek2_Sepp1,Ckmt1_Serinc3,Ckmt1_Sepp1,Plek2_Cyba,Krt5_H2-D1,Ckmt1_Cyba,Igfbp2_Lgals1,Igfbp2_Vim,Lypd2_Vim,Lypd2_Rbm3,Lypd2_Arpc4,Tg_Vim,Tspan1_Xist,Cldn3_Xist,Tg_Ybx1,Ager_Hnrnpf,Ager_Tpm3,Ager_Vim,Cldn3_Serinc3,Cyp2f2_Sepp1,Tspan1_Serinc3,Tspan1_Ybx1,Ces1d_Sepp1,Cbr2_Ybx1,Tg_Klf2,Cldn3_Tpm3,Cyp2f2_Rbm3,Cyp2f2_Hnrnpf,Cbr2_Rbm3,Ces1d_Xist,Cbr2_Hnrnpf,Ces1d_Serinc3,Ifitm1_Sepp1,Hapln1_H2-K1,Hapln1_Ucp2,Hapln1_Xist,Wif1_Slc25a5,Wif1_Xist,Wif1_H2-D1,Scara3_Xist,Scara3_H2-D1,Scara3_H2-K1,Cpe_Atp5b,Col8a1_H2-D1,Col27a1_2010107E04Rik,Cpe_2010107E04Rik,Col27a1_Atp5b,Col27a1_Slc25a5,Col8a1_Slc25a5,Col8a1_Atp5b,Cpe_Atp5f1,Cadm1_H2-K1,Cadm1_2010107E04Rik,Cadm1_Mdh2,1500015O10Rik_Mdh2,1500015O10Rik_Ucp2,1500015O10Rik_Atp5f1,Gpc6_Mdh2 Warning message: In brewer.pal(n = 12, name = "Spectral") : n too large, allowed maximum for palette Spectral is 11 Returning the palette you asked for with that many colors