问题描述
我有四组 A、B、C 和 D，如下所示：
A <- c("ENSG00000103472","ENSG00000130600","ENSG00000177335","ENSG00000177337","ENSG00000178977","ENSG00000180139","ENSG00000180539","ENSG00000187621","ENSG00000188511","ENSG00000197099","ENSG00000203446","ENSG00000203739","ENSG00000203804","ENSG00000204261","ENSG00000204282","ENSG00000204584","ENSG00000205056","ENSG00000205837","ENSG00000206337","ENSG00000213057")
B <- c("ENSG00000146521","ENSG00000165511","ENSG00000174171","ENSG00000176659","ENSG00000179428","ENSG00000179840","ENSG00000204949","ENSG00000223534","ENSG00000223552","ENSG00000223725","ENSG00000226252","ENSG00000226751","ENSG00000226777","ENSG00000227066","ENSG00000227260","ENSG00000227403")
C <- c("ENSG00000167912","ENSG00000168405","ENSG00000172965","ENSG00000177234","ENSG00000177699","ENSG00000177822","ENSG00000181800","ENSG00000181908","ENSG00000183674","ENSG00000189238","ENSG00000196668","ENSG00000196979","ENSG00000197301","ENSG00000203999","ENSG00000206337")
D <- c("ENSG00000122043","ENSG00000162888","ENSG00000167912","ENSG00000176320","ENSG00000179253","ENSG00000185433","ENSG00000205562","ENSG00000213279","ENSG00000214922","ENSG00000215533","ENSG00000218018")
upset 情节给了我以下结果：
library(UpSetR)
mine <- list("A" = A,"B" = B,"C" = C,"D" = D)
upset(fromList(mine),keep.order = TRUE)
但我有兴趣查看特定集合之间的交集。 A & B,A & C,A & D。所以，我是这样做的：
upset(fromList(mine),intersections = list(list("A"),list("B"),list("C"),list("D"),list("A","B"),"C"),"D")),keep.order = TRUE)
但是，A&B 的共同点是 4，A&C 是 4，A&D 是 3。为什么上面的翻转图显示错误的数字？
如何使它正确显示正确的公共数字？我不想要所有集合之间的共同点。
解决方法
数字是正确的！这个问题非常具体和复杂。
有不同的方法来计算集合交叉点的大小：
- “不同”模式
- “相交”模式
- “联合”模式
UpSetR 使用“distinct”模式。
“相交”模式可能是用户所期望的。
ComplexHeatmap 和 ComplexUpset 包允许用户选择使用哪种模式。
我在此处找到了 Jakob Rosenthal 的充分解释https://github.com/hms-dbmi/UpSetR/issues/72，尤其是这张图：
