Entering edit mode
What is the meaning of the first row in $vennCounts, and what is the relationship to the totalTest value of the hypergeometric test?
[1,] 0 0 0 0 0 7692
In the graphic these counts appear as "Others: 7692"
ol <- findOverlapsOfPeaks(ATAC_4C, ATAC_20h, ATAC_72h, ATAC_RSCn, ATAC_Sp, connectedPeaks = c("min"))
tiff(file="Venn_ATAC_4C_Sp_20h_72h_RSCn.tif", width = 7, height = 7, units = 'in', res = 300)
Venn <- makeVennDiagram(ol, totalTest=400000, fill=c("#009E73", "#FF3100", "#F0E442", "#6fa8dc", "#674ea7"), fontfamily ="Helvetica", cat.fontfamily= "Helvetica", cex = 0.8, cat.cex = 1.2) # circle fill color
Venn
col=c("#D55E00", "dark gray") #circle border color
cat.col=c("#D55E00", "dark gray") # label color, keep same as circle border color
dev.off()
$p.value
ATAC_4C ATAC_20h ATAC_72h ATAC_RSCn ATAC_Sp pval
[1,] 0 0 0 1 1 0
[2,] 0 0 1 0 1 0
[3,] 0 0 1 1 0 0
[4,] 0 1 0 0 1 0
[5,] 0 1 0 1 0 0
[6,] 0 1 1 0 0 0
[7,] 1 0 0 0 1 0
[8,] 1 0 0 1 0 0
[9,] 1 0 1 0 0 0
[10,] 1 1 0 0 0 0
$vennCounts
ATAC_4C ATAC_20h ATAC_72h ATAC_RSCn ATAC_Sp Counts
[1,] 0 0 0 0 0 7692
[2,] 0 0 0 0 1 35872
[3,] 0 0 0 1 0 32338
[4,] 0 0 0 1 1 11957
[5,] 0 0 1 0 0 19087
[6,] 0 0 1 0 1 5183
[7,] 0 0 1 1 0 6494
[8,] 0 0 1 1 1 5909
[9,] 0 1 0 0 0 22136
[10,] 0 1 0 0 1 3393
[11,] 0 1 0 1 0 4084
[12,] 0 1 0 1 1 2368
[13,] 0 1 1 0 0 8410
[14,] 0 1 1 0 1 3083
[15,] 0 1 1 1 0 4560
[16,] 0 1 1 1 1 4986
[17,] 1 0 0 0 0 19632
[18,] 1 0 0 0 1 5513
[19,] 1 0 0 1 0 7505
[20,] 1 0 0 1 1 6811
[21,] 1 0 1 0 0 8676
[22,] 1 0 1 0 1 5110
[23,] 1 0 1 1 0 8580
[24,] 1 0 1 1 1 17134
[25,] 1 1 0 0 0 4573
[26,] 1 1 0 0 1 2147
[27,] 1 1 0 1 0 3299
[28,] 1 1 0 1 1 4191
[29,] 1 1 1 0 0 9373
[30,] 1 1 1 0 1 8457
[31,] 1 1 1 1 0 18418
[32,] 1 1 1 1 1 93029
attr(,"class")
[1] "VennCounts"
