retained.duplicates <-
homeologs.pairs %>%
subset(Maize1 != "" & Maize2 != "")
test.goAnnotations.sub1 <-
goAnnotations.sub1[goAnnotations.sub1$gene2 %in% retained.duplicates$Maize1,]
test.goAnnotations.sub2 <-
goAnnotations.sub2[goAnnotations.sub2$gene2 %in% retained.duplicates$Maize2,]
# All EV-Codes
grid.newpage()
g <- draw.pairwise.venn(
area1 = test.goAnnotations.sub1 %>% select(goTerm) %>% distinct() %>% nrow(),
area2 = test.goAnnotations.sub2 %>% select(goTerm) %>% distinct() %>% nrow(),
cross.area = intersect(test.goAnnotations.sub1 %>% select(goTerm), test.goAnnotations.sub2 %>% select(goTerm)) %>% nrow(),
category = c("Maize1", "Maize2"),
lty = rep("blank", 2),
fill = c("light blue", "green"),
alpha = rep(0.5, 2),
cat.pos = c(0, 180),
scaled = FALSE,
euler.d = FALSE,
sep.dist = 0.3,
rotation.degree = 0,
ind = FALSE
)
grid.arrange(gTree(children=g), top="GO Term by Subgenome for Retained Duplicates\n(All EV-Codes)")
# # All EV-Codes, GOSlim only
# grid.newpage()
# g <- draw.pairwise.venn(
# area1 = goAnnotations.sub1 %>% inner_join(go.goSlim.plant, by=c(goTerm = "GOSlimTerm")) %>% select(goTerm) %>% distinct() %>% nrow(),
# area2 = goAnnotations.sub2 %>% inner_join(go.goSlim.plant, by=c(goTerm = "GOSlimTerm")) %>% select(goTerm) %>% distinct() %>% nrow(),
# cross.area = intersect(goAnnotations.sub1 %>% inner_join(go.goSlim.plant, by=c(goTerm = "GOSlimTerm")) %>% select(goTerm),
# goAnnotations.sub2 %>% inner_join(go.goSlim.plant, by=c(goTerm = "GOSlimTerm")) %>% select(goTerm)) %>%
# nrow(),
# category = c("Maize1", "Maize2"),
# lty = rep("blank", 2),
# fill = c("light blue", "green"),
# alpha = rep(0.5, 2),
# cat.pos = c(0, 180),
# scaled = FALSE,
# euler.d = FALSE,
# sep.dist = 0.3,
# rotation.degree = 0,
# ind = FALSE
# )
# grid.arrange(gTree(children=g), top="GO Term by Subgenome\n(All EV-Codes, GOSlim only)")
# # All EV-Codes, MF terms only
# grid.newpage()
# g <- draw.pairwise.venn(
# area1 = goAnnotations.sub1 %>% filter(type=="MF") %>% select(goTerm) %>% distinct() %>% nrow(),
# area2 = goAnnotations.sub2 %>% filter(type=="MF") %>% select(goTerm) %>% distinct() %>% nrow(),
# cross.area = intersect(goAnnotations.sub1 %>% filter(type=="MF") %>% select(goTerm),
# goAnnotations.sub2 %>% filter(type=="MF") %>% select(goTerm)) %>%
# nrow(),
# category = c("Maize1", "Maize2"),
# lty = rep("blank", 2),
# fill = c("light blue", "green"),
# alpha = rep(0.5, 2),
# cat.pos = c(0, 180),
# scaled = FALSE,
# euler.d = FALSE,
# sep.dist = 0.3,
# rotation.degree = 0,
# ind = FALSE
# )
# grid.arrange(gTree(children=g), top="GO Term by Subgenome\n(All EV-Codes, MF only)")
#EXP only
grid.newpage()
g <- draw.pairwise.venn(
area1 = test.goAnnotations.sub1 %>% filter(evCode=="EXP") %>% select(goTerm) %>% distinct() %>% nrow(),
area2 = test.goAnnotations.sub2 %>% filter(evCode=="EXP") %>% select(goTerm) %>% distinct() %>% nrow(),
cross.area = intersect(test.goAnnotations.sub1 %>% filter(evCode=="EXP") %>% select(goTerm),
test.goAnnotations.sub2 %>% filter(evCode=="EXP") %>% select(goTerm)
) %>% nrow(),
category = c("Maize1", "Maize2"),
lty = rep("blank", 2),
fill = c("light blue", "green"),
alpha = rep(0.5, 2),
cat.pos = c(0, 180),
scaled = FALSE,
euler.d = FALSE,
sep.dist = 0.3,
rotation.degree = 0,
ind = FALSE
)
grid.arrange(gTree(children=g), top="GO Term by Subgenome for Retained Duplicates\n(EV-EXP only)")
# #EXP only, GOSlim only
# grid.newpage()
# g <- draw.pairwise.venn(
# area1 = goAnnotations.sub1 %>% inner_join(go.goSlim.plant, by=c(goTerm = "GOSlimTerm")) %>% filter(evCode=="EXP") %>% select(goTerm) %>% distinct() %>% nrow(),
# area2 = goAnnotations.sub2 %>% inner_join(go.goSlim.plant, by=c(goTerm = "GOSlimTerm")) %>% filter(evCode=="EXP") %>% select(goTerm) %>% distinct() %>% nrow(),
# cross.area = intersect(goAnnotations.sub1 %>% inner_join(go.goSlim.plant, by=c(goTerm = "GOSlimTerm"))%>% filter(evCode=="EXP") %>% select(goTerm),
# goAnnotations.sub2 %>% inner_join(go.goSlim.plant, by=c(goTerm = "GOSlimTerm")) %>% filter(evCode=="EXP") %>% select(goTerm)
# ) %>% nrow(),
# category = c("Maize1", "Maize2"),
# lty = rep("blank", 2),
# fill = c("light blue", "green"),
# alpha = rep(0.5, 2),
# cat.pos = c(0, 180),
# scaled = FALSE,
# euler.d = FALSE,
# sep.dist = 0.3,
# rotation.degree = 0,
# ind = FALSE
# )
# grid.arrange(gTree(children=g), top="GO Term by Subgenome\n(EV-EXP, GOSlim only)")
# #EXP only, MF terms only
# grid.newpage()
# g <- draw.pairwise.venn(
# area1 = goAnnotations.sub1 %>% filter(evCode=="EXP") %>% filter(type=="MF") %>% select(goTerm) %>% distinct() %>% nrow(),
# area2 = goAnnotations.sub2 %>% filter(evCode=="EXP") %>% filter(type=="MF") %>% select(goTerm) %>% distinct() %>% nrow(),
# cross.area = intersect(goAnnotations.sub1 %>% filter(evCode=="EXP") %>% filter(type=="MF") %>% select(goTerm),
# goAnnotations.sub2 %>% filter(evCode=="EXP") %>% filter(type=="MF") %>% select(goTerm)
# ) %>% nrow(),
# category = c("Maize1", "Maize2"),
# lty = rep("blank", 2),
# fill = c("light blue", "green"),
# alpha = rep(0.5, 2),
# cat.pos = c(0, 180),
# scaled = FALSE,
# euler.d = FALSE,
# sep.dist = 0.3,
# rotation.degree = 0,
# ind = FALSE
# )
# grid.arrange(gTree(children=g), top="GO Term by Subgenome\n(EV-EXP, MF only)")
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