Update Figures_scRNA_seq.R

Figures_scRNA_seq.R

@@ -14,19 +14,19 @@ library(ggpubr)
 library('introdataviz')
 
 ## full data all the condition 
-full_obj <- readRDS('/DATA_lustre/DATA/HSC_GeneTherapy/Paper_Ana_GE_2023/full_csc_2023.rds')
+full_obj <- readRDS('full_csc_2023.rds')
 
 ## senescence lists
 gmt.obj_s <- read.gmt('senescence_list_paper.gmt')
 gmt.obj_s$term <- factor(gmt.obj$term)
-gmt.obj_s <- gmt.obj_s[gmt.obj_s$term %in% c('FRIDMAN_SENESCENCE_UP', 'SASP_SCHLEICH')
+gmt.obj_s <- gmt.obj_s[gmt.obj_s$term %in% c('SenMayo', 'SASP_SCHLEICH', 'PURCELL')
 table(gmt.obj_s$term)
 
-HALLMARK_TNFA_SIGNALING_VIA_NFKB = c('ABCA1','ACKR3','AREG','ATF3','ATP2B1','B4GALT1','B4GALT5','BCL2A1','BCL3','BCL6','BHLHE40','BIRC2','BIRC3','BMP2','BTG1','BTG2','BTG3','CCL2','CCL20','CCL4','CCL5','CCN1','CCND1','CCNL1','CCRL2','CD44','CD69','CD80','CD83','CDKN1A','CEBPB','CEBPD','CFLAR','CLCF1','CSF1','CSF2','CXCL1','CXCL10','CXCL11','CXCL2','CXCL3','CXCL6','DENND5A','DNAJB4','DRAM1','DUSP1','DUSP2','DUSP4','DUSP5','EDN1','EFNA1','EGR1','EGR2','EGR3','EHD1','EIF1','ETS2','F2RL1','F3','FJX1','FOS','FOSB','FOSL1','FOSL2','FUT4','G0S2','GADD45A','GADD45B','GCH1','GEM','GFPT2','GPR183','HBEGF','HES1','ICAM1','ICOSLG','ID2','IER2','IER3','IER5','IFIH1','IFIT2','IFNGR2','IL12B','IL15RA','IL18','IL1A','IL1B','IL23A','IL6','IL6ST','IL7R','INHBA','IRF1','IRS2','JAG1','JUN','JUNB','KDM6B','KLF10','KLF2','KLF4','KLF6','KLF9','KYNU','LAMB3','LDLR','LIF','LITAF','MAFF','MAP2K3','MAP3K8','MARCKS','MCL1','MSC','MXD1','MYC','NAMPT','NFAT5','NFE2L2','NFIL3','NFKB1','NFKB2','NFKBIA','NFKBIE','NINJ1','NR4A1','NR4A2','NR4A3','OLR1','PANX1','PDE4B','PDLIM5','PER1','PFKFB3','PHLDA1','PHLDA2','PLAU','PLAUR','PLEK','PLK2','PLPP3','PMEPA1','PNRC1','PPP1R15A','PTGER4','PTGS2','PTPRE','PTX3','RCAN1','REL','RELA','RELB','RHOB','RIGI','RIPK2','RNF19B','SAT1','SDC4','SERPINB2','SERPINB8','SERPINE1','SGK1','SIK1','SLC16A6','SLC2A3','SLC2A6','SMAD3','SNN','SOCS3','SOD2','SPHK1','SPSB1','SQSTM1','STAT5A','TANK','TAP1','TGIF1','TIPARP','TLR2','TNC','TNF','TNFAIP2','TNFAIP3','TNFAIP6','TNFAIP8','TNFRSF9','TNFSF9','TNIP1','TNIP2','TRAF1','TRIB1','TRIP10','TSC22D1','TUBB2A','VEGFA','YRDC','ZBTB10','ZC3H12A','ZFP36')
 
-gmt.obj <- list('HALLMARK_TNFA_SIGNALING_VIA_NFKB' = HALLMARK_TNFA_SIGNALING_VIA_NFKB,
-                'FRIDMAN_SENESCENCE_UP' = gmt.obj_s[gmt.obj_s$term == 'FRIDMAN_SENESCENCE_UP',],
-                'SASP_SCHLEICH' = gmt.obj_s[gmt.obj_s$term == 'SASP_SCHLEICH',])
+
+gmt.obj <- list( 'SenMayo' = gmt.obj_s[gmt.obj_s$term == 'SenMayo',],
+                'SASP_SCHLEICH' = gmt.obj_s[gmt.obj_s$term == 'SASP_SCHLEICH',], 
+                'PURCELL' = gmt.obj_s[gmt.obj_s$term == 'PURCELL',]) 
 
 
 ll <- gmt.obj 
@@ -108,9 +108,9 @@ Idents(full_obj) <- 'CSC_clusters'
 
 
 names(ll)
-namex <- list('FRIDMAN_SENESCENCE_UP' = 'FRIDMAN SENESCENCE UP',
-              'SASP_SCHLEICH' = 'SASP SCHLEICH',
-              "HALLMARK_TNFA_SIGNALING_VIA_NFKB" = "HALLMARK TNFA SIGNALING VIA NFKB1")
+namex <- list('SenMayo' =  'SenMayo',
+                'SASP_SCHLEICH' = 'SASP_SCHLEICH', 
+                'PURCELL' = 'PURCELL' )
 
 colrs <- c("RNP NEG"="black",  "RNP HS"="gray20", "GFP-"="grey50", "GFP+"="green3") #"RNP H=grey 36