update

101018

DGIST_compare.R

@@ -56,13 +56,21 @@ scale_color_manual(values = c("#c90000",  "#ea9800",  "#04a327", "#6e0087")) + s
 dev.off()
 
 
+############################################################
+##tool 별 corr plot그리는 code###############################
+############################################################
+source("https://bioconductor.org/biocLite.R")
+biocLite("ggcorrplot")
 
 library(ggcorrplot)
-df <- read.table("cor.txt", sep="\t", header=TRUE)
+setwd("/storage2/Project/CSC/10X/DGIST_data")
+
+df <- read.table("/storage2/Project/CSC/10X/DGIST_data/corr_mark2.txt", sep="\t", header=TRUE)
 rownames(df) <- df$X
 df <- df[-1]
 
-corr <- round(cor(df),2)
+#corr <- round(cor(df),2)
+corr <- cor(df)
 cor.test(df$DGIST, df$CIBERSORT)
 
 # Pearson's product-moment correlation
@@ -76,7 +84,7 @@ cor.test(df$DGIST, df$CIBERSORT)
 #      cor 
 #0.9051184 
 
-pdf("corrplot.pdf", width=10, height=10)
+pdf("corrplot_mark2.pdf", width=10, height=10)
 corrplot(corr, method = "pie",type="upper",tl.col="black", tl.srt=45,addCoef.col = "black")
 dev.off()
 
@@ -228,24 +236,76 @@ dev.off()
 
 
 #DGIST vs Xcell : gene exp / cell type 
-TGgene=c('ALDH1A2','ALOX15','CCL13','CCL17','CCL18','CCL23','CCL24','CD209','CD86','CLEC10A','F13A1','FCER2','IL3RA','SPINT2')
+TGgene=c('02-Sep','ABI2','ACBD3','ACTG1','ADAMTS12','ADD1','ADH1B','ADH5','AHSA1','ALCAM','ALDOA','AMZ2','ANAPC13','ANKFY1','ANXA1','ANXA5','ARCN1','ARF4','ARHGAP6','ARL1','ASAP2','ASCC3','ASPN','ATP5G1','ATP5J','ATP6V0E1','ATP6V1D','ATXN10','ATXN2','BAD','BAG2','BAG3','BUB3','BYSL','C11orf95','C12orf10','C14orf2','C19orf24','C2orf49','C6orf120','CACNA1C','CALR','CANX','CAPN2','CAPNS1','CCDC102B','CCDC53','CCDC90B','CCL8','CCNG1','CDIPT','CDK4','CDK7','CETN2','CISD1','CIZ1','CLEC3B','CNIH4','CNN2','COG7','COPA','COPB1','COPB2','COPS2','COPS7A','COX8A','CRYZL1','CSNK1G3','CSNK2A2','CTNNA1','CUEDC2','CUL7','CUTA','DALRD3','DCTN1','DCTN4','DDA1','DDB1','DDX47','DHX29','DKKL1','DNAJC13','DPT','DPY19L4','DYNC1LI2','DYNLRB1','ECT2','EDA2R','EEF1D','EID1','EIF3I','EIF4G2','EIF6','ELN','EMILIN1','EPN2','ERC1','ERCC1','ERGIC3','ERLIN1','EXOC1','EXOC7','FAF2','FAM160B2','FAM189B','FAM98A','FBXL12','FBXO21','FBXO22','FGF7','FKTN','FSHB','FTO','GANAB','GDF10','GDF5','GLT8D1','GMPR2','GOLGA3','GORASP2','GRSF1','GTF2H5','HADHA','HDLBP','HIC1','HLCS','HOXA3','HPD','HSP90AB1','HSP90B1','HSPA8','HSPB6','HSPB7','IFT46','IGF2BP3','INVS','IPO5','ISCU','ISLR','KDELR1','KDELR2','KIF3B','KLHL9','KRT19','KTN1','LAMP1','LAPTM4A','LGALS1','LMOD1','LRRC15','LTC4S','MANF','MAP3K7','MBTPS1','MBTPS2','MCTS1','MEA1','METTL5','MIF','MINPP1','MLH3','MMADHC','MORF4L2','MPZL1','MRPL15','MRPL17','MRPL40','MRPS11','MRPS33','MTMR2','MYCT1','MYL6','MYL6B','MYOF','MYOZ2','NBR1','NCKAP1','NDUFA8','NDUFB4','NDUFS4','NDUFS5','NETO2','NFATC4','NGRN','NOP10','OCRL','OGN','P4HB','PCDHGB5','PCDHGC3','PEX12','PEX2','PFN2','PGRMC1','PHKG1','PKNOX2','PLS3','POFUT2','POLR2F','POMP','PPP2R1A','PREPL','PRKAG1','PRKG1','PRRC1','PSMB1','PSMB4','PSMB5','PSMB7','PSMC5','PSMD10','PSMD14','PTGIR','PTP4A2','PTPN11','PTTG1IP','RARS','RBMS1','RER1','RFX2','RHOC','RIN2','RING1','RNF7','RPL10','RPL35A','RPL4','RPN2','RPS19','RWDD2B','S100A10','S100A6','S1PR2','SCAMP1','SCFD1','SCRG1','SDF2','SEC61B','SEC61G','SENP5','SGCD','SHFM1','SIX5','SLC35E1','SMAD5','SNTB2','SNUPN','SNX13','SOD1','SPAG16','SPAG7','SPATA7','SPATS2','SPEG','SPIN1','SRPRB','SSBP1','SSR1','ST13','STAM2','STX12','SVEP1','TBC1D17','TBL2','TCF21','TEX261','TFG','THAP10','TIMM17A','TM2D1','TMED1','TMED7','TMED9','TMEM165','TMEM184B','TMEM59','TMEM59L','TMEM87A','TNPO2','TOMM20','TPI1','TPM3','TRAPPC4','TRIM32','TSEN34','TTC37','TUBG2','TXNL1','UFC1','UFD1L','UFSP2','UQCRQ','USO1','VAMP3','VCL','VCP','VIM','VTI1B','WDFY3','YAP1','YIPF2','ZMPSTE24','ZMYM4','ZNF358','ZNF426','ZNF471','ZNF771','ZNHIT1')
 
 for (i in TGgene){
   print(ensemblGenes[ensemblGenes$external_gene_name == i,'ensembl_gene_id'])
 }
 
 
-exp =  DGIST@scale.data["ENSG00000128918",]
+exp =  DGIST@scale.data["ENSG00000138443",]
 
 #TGgene=CIBERSORT celltype marker gene 
-TGgene=c("ENSG00000161905","ENSG00000181374","ENSG00000102970","ENSG00000275385","ENSG00000274736","ENSG00000106178","ENSG00000090659","ENSG00000114013","ENSG00000132514","ENSG00000124491","ENSG00000104921","ENSG00000185291","ENSG00000167642")
+TGgene=c("ENSG00000182827","ENSG00000184009","ENSG00000151388","ENSG00000087274","ENSG00000196616","ENSG00000197894",
+  "ENSG00000100591","ENSG00000170017","ENSG00000149925","ENSG00000196704","ENSG00000129055","ENSG00000185722",
+  "ENSG00000135046","ENSG00000164111","ENSG00000095139","ENSG00000168374","ENSG00000047648","ENSG00000120805",
+  "ENSG00000151693","ENSG00000112249","ENSG00000106819","ENSG00000159199","ENSG00000154723","ENSG00000113732",
+  "ENSG00000100554","ENSG00000130638","ENSG00000204842","ENSG00000002330","ENSG00000112208","ENSG00000151929",
+  "ENSG00000154473","ENSG00000112578","ENSG00000188070","ENSG00000139637","ENSG00000156411","ENSG00000228300",
+  "ENSG00000135974","ENSG00000185127","ENSG00000151067","ENSG00000179218","ENSG00000127022","ENSG00000162909",
+  "ENSG00000126247","ENSG00000150636","ENSG00000137500","ENSG00000108700","ENSG00000113328","ENSG00000103502",
+  "ENSG00000135446","ENSG00000134058","ENSG00000147400","ENSG00000122873","ENSG00000148337","ENSG00000163815",
+  "ENSG00000143771","ENSG00000064666","ENSG00000168434","ENSG00000122218","ENSG00000129083","ENSG00000184432",
+  "ENSG00000166200","ENSG00000111652","ENSG00000176340","ENSG00000205758","ENSG00000151292","ENSG00000070770",
+  "ENSG00000044115","ENSG00000107874","ENSG00000044090","ENSG00000112514","ENSG00000178149","ENSG00000204843",
+  "ENSG00000132912","ENSG00000130311","ENSG00000167986","ENSG00000213782","ENSG00000067248","ENSG00000104901",
+  "ENSG00000138246","ENSG00000143196","ENSG00000156162","ENSG00000135720","ENSG00000125971","ENSG00000114346",
+  "ENSG00000131080","ENSG00000104529","ENSG00000255302","ENSG00000084623","ENSG00000110321","ENSG00000242372",
+  "ENSG00000049540","ENSG00000138080","ENSG00000072134","ENSG00000082805","ENSG00000012061","ENSG00000125991",
+  "ENSG00000107566","ENSG00000090989","ENSG00000182473","ENSG00000113194","ENSG00000158863","ENSG00000160767",
+  "ENSG00000119812","ENSG00000127452","ENSG00000135108","ENSG00000167196","ENSG00000140285","ENSG00000106692",
+  "ENSG00000131808","ENSG00000140718","ENSG00000089597","ENSG00000266524","ENSG00000125965","ENSG00000016864",
+  "ENSG00000100938","ENSG00000090615","ENSG00000115806","ENSG00000132463","ENSG00000272047","ENSG00000084754",
+  "ENSG00000115677","ENSG00000177374","ENSG00000159267","ENSG00000105997","ENSG00000158104","ENSG00000096384",
+  "ENSG00000166598","ENSG00000109971","ENSG00000004776","ENSG00000173641","ENSG00000118096","ENSG00000136231",
+  "ENSG00000119509","ENSG00000065150","ENSG00000136003","ENSG00000129009","ENSG00000105438","ENSG00000136240",
+  "ENSG00000101350","ENSG00000198642","ENSG00000171345","ENSG00000126777","ENSG00000185896","ENSG00000068697",
+  "ENSG00000100097","ENSG00000163431","ENSG00000172061","ENSG00000213316","ENSG00000145050","ENSG00000135341",
+  "ENSG00000140943","ENSG00000012174","ENSG00000232119","ENSG00000124733","ENSG00000138382","ENSG00000240972",
+  "ENSG00000107789","ENSG00000119684","ENSG00000168288","ENSG00000123562","ENSG00000197965","ENSG00000137547",
+  "ENSG00000158042","ENSG00000185608","ENSG00000181991","ENSG00000090263","ENSG00000087053","ENSG00000120279",
+  "ENSG00000092841","ENSG00000196465","ENSG00000138119","ENSG00000172399","ENSG00000188554","ENSG00000061676",
+  "ENSG00000119421","ENSG00000065518","ENSG00000164258","ENSG00000168653","ENSG00000171208","ENSG00000100968",
+  "ENSG00000182768","ENSG00000182117","ENSG00000122126","ENSG00000106809","ENSG00000185624","ENSG00000276547",
+  "ENSG00000240184","ENSG00000108733","ENSG00000164751","ENSG00000070087","ENSG00000101856","ENSG00000164776",
+  "ENSG00000165495","ENSG00000102024","ENSG00000186866","ENSG00000100142","ENSG00000132963","ENSG00000105568",
+  "ENSG00000138078","ENSG00000181929","ENSG00000185532","ENSG00000164244","ENSG00000008018","ENSG00000159377",
+  "ENSG00000100804","ENSG00000136930","ENSG00000087191","ENSG00000101843","ENSG00000115233","ENSG00000160013",
+  "ENSG00000184007","ENSG00000179295","ENSG00000183255","ENSG00000113643","ENSG00000153250","ENSG00000157916",
+  "ENSG00000087903","ENSG00000155366","ENSG00000132669","ENSG00000204227","ENSG00000114125","ENSG00000147403",
+  "ENSG00000182899","ENSG00000174444","ENSG00000118705","ENSG00000105372","ENSG00000156253","ENSG00000197747",
+  "ENSG00000197956","ENSG00000267534","ENSG00000085365","ENSG00000092108","ENSG00000164106","ENSG00000132581",
+  "ENSG00000106803","ENSG00000132432","ENSG00000119231","ENSG00000170624","ENSG00000177045","ENSG00000127526",
+  "ENSG00000113658","ENSG00000168807","ENSG00000169371","ENSG00000071189","ENSG00000142168","ENSG00000144451",
+  "ENSG00000091640","ENSG00000042317","ENSG00000123352","ENSG00000072195","ENSG00000106723","ENSG00000144867",
+  "ENSG00000106028","ENSG00000124783","ENSG00000100380","ENSG00000115145","ENSG00000117758","ENSG00000165124",
+  "ENSG00000104946","ENSG00000106638","ENSG00000118526","ENSG00000144043","ENSG00000114354","ENSG00000129028",
+  "ENSG00000134375","ENSG00000162604","ENSG00000099203","ENSG00000134970","ENSG00000184840","ENSG00000134851",
+  "ENSG00000198792","ENSG00000116209","ENSG00000105696","ENSG00000103978","ENSG00000105576","ENSG00000173726",
+  "ENSG00000111669","ENSG00000143549","ENSG00000196655","ENSG00000119401","ENSG00000170892","ENSG00000198677",
+  "ENSG00000037042","ENSG00000091164","ENSG00000143222","ENSG00000109775","ENSG00000164405","ENSG00000138768",
+  "ENSG00000049245","ENSG00000035403","ENSG00000165280","ENSG00000026025","ENSG00000100568","ENSG00000163625",
+  "ENSG00000137693","ENSG00000130733","ENSG00000084073","ENSG00000146463","ENSG00000198816","ENSG00000130818",
+  "ENSG00000196263","ENSG00000179965","ENSG00000106400")
+
+
 
 for (i in TGgene){
   test = DGIST@scale.data[i,]
   exp <- rbind(exp,test)
 }
 
-celltypes = "iDC"
+celltypes = "Smooth muscle"
 
 pdf(paste0("DGIST_Xcell_",celltypes,".pdf"),width=12, height=9)
 df = data.frame(x=DGIST@dr$tsne@cell.embeddings[, "tSNE_1"],