Figure 7: Genes in AC toxicity-associated loci respond to TOP2i.

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Last updated: 2024-02-06

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Knit directory: Cardiotoxicity/

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---

library(tidyverse)
library(gridtext)
library(scales)
library(kableExtra)
library(qvalue)
library(data.table)
library(ComplexHeatmap)
library(readr)
library(limma)
library(edgeR)

drug_palc <- c("#8B006D","#DF707E","#F1B72B", "#3386DD","#707031","#41B333")
drug_pal_fact <- c("#8B006D" ,"#DF707E", "#F1B72B" ,"#3386DD", "#707031","#41B333")

cpmcounts <- readRDS("data/cpmcount.RDS")
DEG_cormotif <- readRDS("data/DEG_cormotif.RDS")
list2env(DEG_cormotif,envir=.GlobalEnv)

<environment: R_GlobalEnv>

backGL <- read.csv("data/backGL.txt", row.names =1)
col_fun1 = circlize::colorRamp2(c(-1, 3), c("white", "purple"))
col_funFC= circlize::colorRamp2(c(-2,0, 2), c("darkgreen","white", "darkorange2"))
col_funTOX = circlize::colorRamp2(c(-1,0, 1), c("darkviolet", "white","firebrick4"))


DOXrespGene <- readRDS("output/DOXreQTLs.RDS")
toplistall <- readRDS("data/toplistall.RDS")

list2env(DEG_cormotif,envir=.GlobalEnv)

<environment: R_GlobalEnv>

counts_v8_heart_left_ventricle_gct <- readRDS("output/counts_v8_heart_left_ventricle_gct.RDS")
names_gtex_genes <- counts_v8_heart_left_ventricle_gct %>% 
  dplyr::select(Name, Description)
gtex_counts_matrix<- counts_v8_heart_left_ventricle_gct %>% 
  column_to_rownames("Name") %>% 
  dplyr::select(!id) %>% 
  dplyr::select(!Description) %>% 
  as.matrix()
  
# cpm <- cpm(gtex_counts_matrix)
lcpm <- cpm(gtex_counts_matrix, log=TRUE)  ### for determining the basic cutoffs

row_means <- rowMeans(lcpm)
gtex_x <- lcpm[row_means > 0,]
GTEX_heartLV_log2cpm <- gtex_x %>% 
  as.data.frame() %>%
  mutate(Name = rownames(gtex_x)) %>% 
  left_join(.,names_gtex_genes, by =c("Name"))





SGWAS_order_frame <- read.csv("output/SGWAS_top50_order.csv", row.names = 1)

col_fun5 = circlize::colorRamp2(c(0, 5), c("white", "purple"))
## supplement 1
chrom_reg_Seoane <- read_csv(file = "data/Seonane2019supp1.txt",col_types = cols(...1 = col_skip()))
Seoane_2019 <- chrom_reg_Seoane[,2]
names(Seoane_2019) <- "ENTREZID"
Chrom_reg <- data.frame("entrez"=(unique(Seoane_2019$ENTREZID)))

Sup4seoane <- read.csv("output/Sup4seoane.csv", row.names = 1)
DOX_reg <- Sup4seoane  %>% 
  filter(pval.expAnth<0.05) %>% 
  distinct(entrez, .keep_all = TRUE) %>% 
  dplyr::select(entrez)
base_egene <-readRDS("output/knowles4.RDS")
resp_egene <-readRDS("output/knowles5.RDS")

Figure 7: Genes in AC toxicity-associated loci respond to TOP2i.

24 hours

orderit <- data.frame(SYMBOL=c(SGWAS_order_frame$SYMBOL,'RARG',
                        'TNS2', 
                        'ZNF740',
                        'SLC28A3',
                        'RMI1',
                        'EEF1B2',
                        'FRS2', 
                        'HDDC2')) %>% 
  left_join(.,backGL) %>% 
  mutate(motif= if_else(ENTREZID %in% motif_ER, "ER", if_else(ENTREZID %in% motif_LR, "LR",if_else(ENTREZID %in% motif_TI, "TI", "NR" )))) %>% 
  mutate(chrom_gene= if_else(ENTREZID %in% Chrom_reg$entrez,"yes","no")) %>% 
  mutate(Dox_respegene= if_else(ENTREZID %in% resp_egene$entrezgene_id, "yes","no")) %>% 
  mutate(ACchrom_gene= if_else(ENTREZID %in%  DOX_reg$entrez,"yes","no")) %>%  
  mutate(gTEX_heart=if_else(SYMBOL %in% GTEX_heartLV_log2cpm$Description,  "yes","no"))




toplistall %>% 
    mutate(drug=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  filter(ENTREZID %in% orderit$ENTREZID) %>% 
   filter(time =="24_hours") %>% 
  dplyr::select(ENTREZID , id,logFC, adj.P.Val, SYMBOL) 

             ENTREZID  id        logFC    adj.P.Val  SYMBOL
3958...1         3958 DNR -2.841654211 1.243290e-13  LGALS3
55020...2       55020 DNR  1.333658801 1.747225e-12   TTC38
5095...3         5095 DNR  1.071448603 1.388146e-07    PCCA
29899...4       29899 DNR  1.954225576 4.986630e-07   GPSM2
23371...5       23371 DNR  1.604978233 1.056163e-06    TNS2
57161...6       57161 DNR -2.383146876 3.370044e-06   PELI2
283337...7     283337 DNR -0.579733508 1.525722e-04  ZNF740
150383...8     150383 DNR  1.104262721 1.726928e-04   CDPF1
80856...9       80856 DNR  0.822616727 3.110247e-04    LNPK
4023...10        4023 DNR  1.549451664 5.464607e-04     LPL
51020...11      51020 DNR  0.837500708 1.303926e-03   HDDC2
23262...12      23262 DNR  0.672772048 1.871912e-03 PPIP5K2
10818...13      10818 DNR -0.546865539 1.991410e-03    FRS2
6272...14        6272 DNR  0.621888001 5.362112e-03   SORT1
5916...15        5916 DNR -1.329791599 7.072597e-03    RARG
54826...16      54826 DNR  0.590225431 9.667914e-03    GIN1
78996...17      78996 DNR -0.386375935 1.795971e-02   CYREN
9620...18        9620 DNR  0.363295608 3.669460e-02  CELSR1
80010...19      80010 DNR  0.671889247 4.031601e-02    RMI1
23151...20      23151 DNR  0.436443420 4.741931e-02  GRAMD4
23155...21      23155 DNR  0.337151049 5.197844e-02   CLCC1
64078...22      64078 DNR  1.330462721 5.950696e-02 SLC28A3
10499...23      10499 DNR  0.411899518 6.955554e-02   NCOA2
54477...24      54477 DNR  0.487103345 7.152302e-02 PLEKHA5
23327...25      23327 DNR -0.256622161 8.379995e-02  NEDD4L
4692...26        4692 DNR  0.226204661 1.454533e-01     NDN
57110...27      57110 DNR -0.448716677 3.213072e-01  PLAAT1
344595...28    344595 DNR -0.399962237 4.100997e-01    DUBR
1933...29        1933 DNR -0.107304755 4.912870e-01  EEF1B2
5066...30        5066 DNR  0.154685819 5.472580e-01     PAM
323...31          323 DNR -0.210918044 5.566906e-01   APBB2
80059...32      80059 DNR -0.239094603 6.889705e-01  LRRTM4
8803...33        8803 DNR  0.080349938 7.278560e-01  SUCLA2
8214...34        8214 DNR -0.108231532 7.767081e-01   DGCR6
7991...35        7991 DNR  0.040113972 8.234825e-01   TUSC3
108...36          108 DNR -0.126695676 8.273045e-01   ADCY2
79730...37      79730 DNR -0.057772199 9.021996e-01   NSUN7
11128...38      11128 DNR  0.029517711 9.059731e-01  POLR3A
3958...39        3958 DOX -2.592937478 2.490015e-12  LGALS3
55020...40      55020 DOX  1.283014820 2.916892e-12   TTC38
29899...41      29899 DOX  2.518139384 2.101681e-09   GPSM2
5095...42        5095 DOX  1.010845341 2.818499e-07    PCCA
23371...43      23371 DOX  1.598507639 6.706429e-07    TNS2
57161...44      57161 DOX -2.341492097 3.836758e-06   PELI2
4023...45        4023 DOX  1.808675205 7.124618e-05     LPL
80856...46      80856 DOX  0.895190712 8.678073e-05    LNPK
10818...47      10818 DOX -0.676539058 1.291338e-04    FRS2
78996...48      78996 DOX -0.537877803 7.555844e-04   CYREN
150383...49    150383 DOX  0.858362938 2.193138e-03   CDPF1
9620...50        9620 DOX  0.517275591 2.869762e-03  CELSR1
51020...51      51020 DOX  0.701624821 5.731184e-03   HDDC2
283337...52    283337 DOX -0.381694054 1.117693e-02  ZNF740
23155...53      23155 DOX  0.405344826 1.791996e-02   CLCC1
23151...54      23151 DOX  0.508471630 1.886110e-02  GRAMD4
6272...55        6272 DOX  0.534740395 1.924261e-02   SORT1
23262...56      23262 DOX  0.461885237 2.888855e-02 PPIP5K2
64078...57      64078 DOX  1.500098762 2.987324e-02 SLC28A3
80010...58      80010 DOX  0.668904577 3.576733e-02    RMI1
5916...59        5916 DOX -0.964405340 5.402876e-02    RARG
54826...60      54826 DOX  0.421260779 5.998781e-02    GIN1
1933...61        1933 DOX -0.212731820 1.537205e-01  EEF1B2
7991...62        7991 DOX -0.205234135 2.053194e-01   TUSC3
54477...63      54477 DOX  0.334744068 2.250581e-01 PLEKHA5
79730...64      79730 DOX  0.476855272 2.404724e-01   NSUN7
344595...65    344595 DOX -0.524001048 2.637491e-01    DUBR
80059...66      80059 DOX -0.569911090 2.893850e-01  LRRTM4
4692...67        4692 DOX  0.144561267 3.736745e-01     NDN
8214...68        8214 DOX -0.302754712 3.788465e-01   DGCR6
57110...69      57110 DOX -0.354560827 4.421703e-01  PLAAT1
10499...70      10499 DOX  0.147512070 5.431318e-01   NCOA2
23327...71      23327 DOX -0.080177636 6.273533e-01  NEDD4L
8803...72        8803 DOX -0.087400124 7.094227e-01  SUCLA2
11128...73      11128 DOX  0.060765550 7.943625e-01  POLR3A
108...74          108 DOX  0.127672688 8.270659e-01   ADCY2
5066...75        5066 DOX  0.059664456 8.344395e-01     PAM
323...76          323 DOX -0.031367303 9.393574e-01   APBB2
3958...77        3958 EPI -2.258936236 2.519057e-10  LGALS3
55020...78      55020 EPI  0.974047987 7.331358e-09   TTC38
57161...79      57161 EPI -2.714417489 2.189093e-07   PELI2
29899...80      29899 EPI  1.863235071 1.590451e-06   GPSM2
23371...81      23371 EPI  1.548244317 2.483790e-06    TNS2
5095...82        5095 EPI  0.829217065 1.522752e-05    PCCA
9620...83        9620 EPI  0.673682504 1.442416e-04  CELSR1
10818...84      10818 EPI -0.662974585 2.169251e-04    FRS2
80856...85      80856 EPI  0.839945811 2.618033e-04    LNPK
150383...86    150383 EPI  0.942381848 1.099590e-03   CDPF1
23151...87      23151 EPI  0.734875425 1.137112e-03  GRAMD4
51020...88      51020 EPI  0.832885435 1.421275e-03   HDDC2
4023...89        4023 EPI  1.351101119 2.328703e-03     LPL
54826...90      54826 EPI  0.674858946 3.507401e-03    GIN1
23262...91      23262 EPI  0.602541437 5.337053e-03 PPIP5K2
283337...92    283337 EPI -0.415051660 7.118210e-03  ZNF740
5916...93        5916 EPI -1.219583078 1.479648e-02    RARG
64078...94      64078 EPI  1.702459586 1.707977e-02 SLC28A3
23155...95      23155 EPI  0.369459458 3.478725e-02   CLCC1
6272...96        6272 EPI  0.464185845 4.419093e-02   SORT1
54477...97      54477 EPI  0.512315022 6.054740e-02 PLEKHA5
78996...98      78996 EPI -0.300441979 7.403190e-02   CYREN
7991...99        7991 EPI -0.242241759 1.322443e-01   TUSC3
80010...100     80010 EPI  0.469909001 1.524626e-01    RMI1
1933...101       1933 EPI -0.213535720 1.551221e-01  EEF1B2
11128...102     11128 EPI  0.224307657 2.966829e-01  POLR3A
79730...103     79730 EPI  0.417825538 3.192457e-01   NSUN7
4692...104       4692 EPI -0.153538531 3.515660e-01     NDN
8214...105       8214 EPI -0.277219655 4.398229e-01   DGCR6
57110...106     57110 EPI -0.339243025 4.802483e-01  PLAAT1
323...107         323 EPI -0.187249253 6.196852e-01   APBB2
23327...108     23327 EPI -0.075188817 6.598565e-01  NEDD4L
10499...109     10499 EPI  0.100464458 7.011245e-01   NCOA2
344595...110   344595 EPI -0.182858257 7.439904e-01    DUBR
8803...111       8803 EPI -0.071967777 7.700056e-01  SUCLA2
80059...112     80059 EPI -0.148755480 8.211226e-01  LRRTM4
5066...113       5066 EPI -0.045912799 8.793958e-01     PAM
108...114         108 EPI -0.039274665 9.511661e-01   ADCY2
29899...115     29899 MTX  1.934044382 3.815931e-06   GPSM2
4023...116       4023 MTX  1.451134843 5.826444e-03     LPL
80010...117     80010 MTX  1.092226550 6.604137e-03    RMI1
5095...118       5095 MTX  0.577769680 7.822416e-03    PCCA
80856...119     80856 MTX  0.685663398 1.284470e-02    LNPK
283337...120   283337 MTX -0.280222769 1.954044e-01  ZNF740
10818...121     10818 MTX -0.303886126 2.378802e-01    FRS2
79730...122     79730 MTX  0.628036510 2.868955e-01   NSUN7
3958...123       3958 MTX -0.499180352 3.094334e-01  LGALS3
51020...124     51020 MTX  0.366332291 3.373271e-01   HDDC2
23327...125     23327 MTX  0.198830941 3.917168e-01  NEDD4L
9620...126       9620 MTX  0.208898350 4.712695e-01  CELSR1
64078...127     64078 MTX  0.768540550 4.758212e-01 SLC28A3
57161...128     57161 MTX -0.611530252 5.080329e-01   PELI2
5066...129       5066 MTX  0.250853051 5.499338e-01     PAM
23151...130     23151 MTX  0.209526820 5.825203e-01  GRAMD4
23155...131     23155 MTX  0.164554919 5.877302e-01   CLCC1
8803...132       8803 MTX  0.173292448 6.485778e-01  SUCLA2
80059...133     80059 MTX -0.403073184 6.821231e-01  LRRTM4
6272...134       6272 MTX  0.179183592 6.859679e-01   SORT1
5916...135       5916 MTX -0.340441408 7.425170e-01    RARG
55020...136     55020 MTX  0.085053540 7.601342e-01   TTC38
150383...137   150383 MTX -0.154959612 7.638427e-01   CDPF1
7991...138       7991 MTX  0.093568355 7.664325e-01   TUSC3
108...139         108 MTX  0.297466826 7.704286e-01   ADCY2
57110...140     57110 MTX  0.264958653 7.734792e-01  PLAAT1
8214...141       8214 MTX  0.189812119 7.812516e-01   DGCR6
1933...142       1933 MTX  0.074340382 8.149139e-01  EEF1B2
54826...143     54826 MTX -0.107587669 8.166223e-01    GIN1
23371...144     23371 MTX  0.132833588 8.258590e-01    TNS2
78996...145     78996 MTX -0.079577280 8.278189e-01   CYREN
23262...146     23262 MTX  0.094249849 8.424378e-01 PPIP5K2
323...147         323 MTX  0.133742960 8.617852e-01   APBB2
54477...148     54477 MTX  0.102791888 8.679409e-01 PLEKHA5
11128...149     11128 MTX -0.065059234 8.900008e-01  POLR3A
10499...150     10499 MTX  0.065432833 9.015410e-01   NCOA2
344595...151   344595 MTX -0.094804211 9.359175e-01    DUBR
4692...152       4692 MTX  0.024324107 9.507869e-01     NDN
23371...153     23371 TRZ -0.360682790 9.999716e-01    TNS2
283337...154   283337 TRZ -0.182311739 9.999716e-01  ZNF740
5916...155       5916 TRZ -0.416339236 9.999716e-01    RARG
29899...156     29899 TRZ  0.234391483 9.999716e-01   GPSM2
4023...157       4023 TRZ  0.314414654 9.999716e-01     LPL
54826...158     54826 TRZ -0.147747416 9.999716e-01    GIN1
80856...159     80856 TRZ  0.154476640 9.999716e-01    LNPK
23151...160     23151 TRZ -0.128233102 9.999716e-01  GRAMD4
79730...161     79730 TRZ -0.218396111 9.999716e-01   NSUN7
9620...162       9620 TRZ -0.105210839 9.999716e-01  CELSR1
64078...163     64078 TRZ -0.302421643 9.999716e-01 SLC28A3
78996...164     78996 TRZ -0.077524620 9.999716e-01   CYREN
57161...165     57161 TRZ  0.238798361 9.999716e-01   PELI2
150383...166   150383 TRZ -0.102010613 9.999716e-01   CDPF1
323...167         323 TRZ -0.127795059 9.999716e-01   APBB2
51020...168     51020 TRZ  0.096587761 9.999716e-01   HDDC2
55020...169     55020 TRZ -0.049872370 9.999716e-01   TTC38
10499...170     10499 TRZ -0.076894497 9.999716e-01   NCOA2
1933...171       1933 TRZ  0.045717271 9.999716e-01  EEF1B2
6272...172       6272 TRZ  0.072173304 9.999716e-01   SORT1
80010...173     80010 TRZ  0.089587489 9.999716e-01    RMI1
3958...174       3958 TRZ -0.086684248 9.999716e-01  LGALS3
80059...175     80059 TRZ  0.137665553 9.999716e-01  LRRTM4
23327...176     23327 TRZ -0.037600446 9.999716e-01  NEDD4L
8803...177       8803 TRZ  0.047787071 9.999716e-01  SUCLA2
5095...178       5095 TRZ -0.035722392 9.999716e-01    PCCA
23262...179     23262 TRZ  0.043344764 9.999716e-01 PPIP5K2
8214...180       8214 TRZ  0.066369745 9.999716e-01   DGCR6
10818...181     10818 TRZ  0.034157048 9.999716e-01    FRS2
7991...182       7991 TRZ -0.028941499 9.999716e-01   TUSC3
4692...183       4692 TRZ -0.023636849 9.999716e-01     NDN
11128...184     11128 TRZ  0.028833971 9.999716e-01  POLR3A
54477...185     54477 TRZ -0.035791323 9.999716e-01 PLEKHA5
108...186         108 TRZ -0.043025639 9.999716e-01   ADCY2
57110...187     57110 TRZ  0.031961542 9.999716e-01  PLAAT1
23155...188     23155 TRZ -0.005764121 9.999716e-01   CLCC1
344595...189   344595 TRZ -0.007991521 9.999716e-01    DUBR
5066...190       5066 TRZ -0.001493139 9.999716e-01     PAM

GWASabsFCsig <- 
  toplistall %>% 
    mutate(drug=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  filter(ENTREZID %in% orderit$ENTREZID) %>% 
   filter(time =="24_hours") %>% 
  dplyr::select(ENTREZID , id,logFC, adj.P.Val, SYMBOL)  %>%
  pivot_wider(id_cols=id, 
              names_from = SYMBOL, 
              values_from =adj.P.Val)
  
gwas_sig_mat <- GWASabsFCsig %>% 
   column_to_rownames(var="id") %>%
  dplyr::select(orderit$SYMBOL) %>%
  as.matrix()
 

GWASabsFC <- toplistall %>% 
  
  # filter(id !="TRZ") %>% 
  filter(time=="24_hours") %>% 
  mutate(logFC= logFC*(-1)) %>%
  filter(ENTREZID %in% orderit$ENTREZID) %>% 
  dplyr::select(SYMBOL ,time, id, logFC) %>% 
  pivot_wider(id_cols=id, 
              names_from = SYMBOL, 
              values_from = logFC) %>% 
  column_to_rownames(var="id") %>%
  dplyr::select(orderit$SYMBOL) %>%
  as.matrix()

study_anno <- data.frame(Study=c(rep("GWAS",35),rep("TWAS",3)),motif=orderit$motif,chrom_gene=orderit$chrom_gene,Dox_respegene=orderit$Dox_respegene, ACchrom_gene=orderit$ACchrom_gene,gTEX_heart=orderit$gTEX_heart)
rownames(study_anno) <- colnames(GWASabsFC)
ht <- HeatmapAnnotation(df = study_anno,
              col = list(Study=c("GWAS"="darkorange","TWAS"= "blueviolet"),
                         motif = c("LR"="#00BFC4", "NR"="#C77CFF", "ER"="#F8766D", "TI"="#7CAE00"),
chrom_gene=c("yes"="darkred","no"="pink"),
Dox_respegene=c("yes"="darkred","no"="pink"),
ACchrom_gene=c("yes"="darkred","no"="pink"),
gTEX_heart=c("yes"="darkred","no"="pink")))

Heatmap(GWASabsFC, name = "Fold change\nvalues", 
         cluster_rows = FALSE,
        cluster_columns = FALSE, 
        row_names_side = "left",
        col = col_funFC,
        row_order = c('DOX','EPI','DNR', 'MTX','TRZ'),
        column_title = "24 hours Fold Change of AC-toxicity associated loci", 
        column_title_side = "top",
        column_title_gp = gpar(fontsize = 16, fontface = "bold"),
        column_order= orderit$SYMBOL,
        bottom_annotation = ht,
        
        column_names_rot = 90, 
        column_names_gp = gpar(fontsize = 12,fontface="italic"),
        column_names_centered =TRUE,
         cell_fun = function(j, i, x, y, width, height, fill) {
        if(gwas_sig_mat[i, j] <0.05)
            grid.text("*", x, y, gp = gpar(fontsize = 20))
})

Past versions of "Finfig_hm 24 hours-1.png"

Version	Author	Date
7308a2e	reneeisnowhere	2024-02-06

GWASabsFCsig_3 <- 
  toplistall %>% 
    mutate(drug=factor(id, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>% 
  filter(ENTREZID %in% orderit$ENTREZID) %>% 
   filter(time =="3_hours") %>% 
  dplyr::select(ENTREZID , id,logFC, adj.P.Val, SYMBOL)  %>%
  pivot_wider(id_cols=id, 
              names_from = SYMBOL, 
              values_from =adj.P.Val)
  
gwas_sig_mat_3 <- GWASabsFCsig_3 %>% 
   column_to_rownames(var="id") %>%
  dplyr::select(orderit$SYMBOL) %>%
  as.matrix()
 

GWASabsFC_3 <- toplistall %>% 
  
  # filter(id !="TRZ") %>% 
  filter(time=="3_hours") %>% 
  mutate(logFC= logFC*(-1)) %>%
  filter(ENTREZID %in% orderit$ENTREZID) %>% 
  dplyr::select(SYMBOL ,time, id, logFC) %>% 
  pivot_wider(id_cols=id, 
              names_from = SYMBOL, 
              values_from = logFC) %>% 
  column_to_rownames(var="id") %>%
  dplyr::select(orderit$SYMBOL) %>%
  as.matrix()

# study_anno <- data.frame(Study=c(rep("GWAS",35),rep("TWAS",3)),motif=orderit$motif,chrom_gene=orderit$chrom_gene,Dox_respegene=orderit$Dox_respegene, ACchrom_gene=orderit$ACchrom_gene,gTEX_heart=orderit$gTEX_heart)
# rownames(study_anno) <- colnames(GWASabsFC)
# ht <- HeatmapAnnotation(df = study_anno,
#               col = list(Study=c("GWAS"="darkorange","TWAS"= "blueviolet"),
#                          motif = c("LR"="#00BFC4", "NR"="#C77CFF", "ER"="#F8766D", "TI"="#7CAE00"),
# chrom_gene=c("yes"="darkred","no"="pink"),
# Dox_respegene=c("yes"="darkred","no"="pink"),
# ACchrom_gene=c("yes"="darkred","no"="pink"),
# gTEX_heart=c("yes"="darkred","no"="pink")))

Heatmap(GWASabsFC_3, name = "Fold change\nvalues", 
         cluster_rows = FALSE,
        cluster_columns = FALSE, 
        row_names_side = "left",
        col = col_funFC,
        row_order = c('DOX','EPI','DNR', 'MTX','TRZ'),
        column_title = "3 hours Log2 Foldchange of AC-toxicity associated loci", 
        column_title_side = "top",
        column_title_gp = gpar(fontsize = 16, fontface = "bold"),
        column_order= orderit$SYMBOL,
        bottom_annotation = ht,
        
        column_names_rot = 90, 
        column_names_gp = gpar(fontsize = 12,fontface="italic"),
        column_names_centered =TRUE,
         cell_fun = function(j, i, x, y, width, height, fill) {
        if(gwas_sig_mat_3[i, j] <0.05)
            grid.text("*", x, y, gp = gpar(fontsize = 20))
})

Past versions of "Finfig_hm 3 hours-1.png"

Version	Author	Date
7308a2e	reneeisnowhere	2024-02-06

More analysis GWAS and TWAS SNPs found in the Schneider data at this link.

Session information

sessionInfo()

R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] edgeR_3.42.4          limma_3.56.2          ComplexHeatmap_2.16.0
 [4] data.table_1.14.8     qvalue_2.32.0         kableExtra_1.3.4     
 [7] scales_1.3.0          gridtext_0.1.5        lubridate_1.9.3      
[10] forcats_1.0.0         stringr_1.5.0         dplyr_1.1.3          
[13] purrr_1.0.2           readr_2.1.4           tidyr_1.3.0          
[16] tibble_3.2.1          ggplot2_3.4.4         tidyverse_2.0.0      
[19] workflowr_1.7.1      

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0    viridisLite_0.4.2   fastmap_1.1.1      
 [4] promises_1.2.1      digest_0.6.33       timechange_0.2.0   
 [7] lifecycle_1.0.4     cluster_2.1.4       processx_3.8.2     
[10] magrittr_2.0.3      compiler_4.3.1      rlang_1.1.2        
[13] sass_0.4.7          tools_4.3.1         utf8_1.2.4         
[16] yaml_2.3.7          knitr_1.45          bit_4.0.5          
[19] plyr_1.8.9          xml2_1.3.5          RColorBrewer_1.1-3 
[22] withr_3.0.0         BiocGenerics_0.46.0 stats4_4.3.1       
[25] fansi_1.0.5         git2r_0.32.0        colorspace_2.1-0   
[28] iterators_1.0.14    cli_3.6.1           rmarkdown_2.25     
[31] crayon_1.5.2        generics_0.1.3      rstudioapi_0.15.0  
[34] httr_1.4.7          reshape2_1.4.4      tzdb_0.4.0         
[37] rjson_0.2.21        cachem_1.0.8        splines_4.3.1      
[40] rvest_1.0.3         parallel_4.3.1      matrixStats_1.1.0  
[43] vctrs_0.6.4         webshot_0.5.5       jsonlite_1.8.7     
[46] callr_3.7.3         IRanges_2.34.1      hms_1.1.3          
[49] GetoptLong_1.0.5    S4Vectors_0.38.2    bit64_4.0.5        
[52] clue_0.3-65         magick_2.8.1        systemfonts_1.0.5  
[55] locfit_1.5-9.8      foreach_1.5.2       jquerylib_0.1.4    
[58] glue_1.6.2          codetools_0.2-19    ps_1.7.5           
[61] shape_1.4.6         stringi_1.7.12      gtable_0.3.4       
[64] later_1.3.1         munsell_0.5.0       pillar_1.9.0       
[67] htmltools_0.5.7     circlize_0.4.15     R6_2.5.1           
[70] doParallel_1.0.17   rprojroot_2.0.4     vroom_1.6.5        
[73] lattice_0.22-5      evaluate_0.23       highr_0.10         
[76] png_0.1-8           httpuv_1.6.12       bslib_0.6.1        
[79] Rcpp_1.0.11         svglite_2.1.2       whisker_0.4.1      
[82] xfun_0.41           fs_1.6.3            getPass_0.2-2      
[85] pkgconfig_2.0.3     GlobalOptions_0.1.2