custom-R-functions/plot_helpers.R at master · amitjavilaventura/custom-R-functions · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
# Plot helpers

# Highlight areas of 2D Venn
venn2_highlight <- function(highlight = c("AB", "AnoB"), color = c("red", "pink"),
                            label = NULL, label.pos = "bottom.right", label.face = "italic", label.size = 13, label.col = "black",
                            line.col = "black"){

  library(polyclip)
  library(VennDiagram)
  library(ggplot2)

  invisible(vp <- VennDiagram::draw.pairwise.venn(area1 = 2, area2 = 2, cross.area = 1, category = rep("", 2), cex = 0, label.col = NA, scaled = F, fill = NA, margin = 0, disable.logging = T))

  A <- list(list(x = as.vector(vp[[1]][[1]]), y = as.vector(vp[[1]][[2]])))
  B <- list(list(x = as.vector(vp[[2]][[1]]), y = as.vector(vp[[2]][[2]])))

  AB <- polyclip::polyclip(A,B)

  ABC     <- polyclip::polyclip(A,B) %>% polyclip::polyclip(., C)

  AnoB <- polyclip::polyclip(A,B, op = "minus")
  noAB <- polyclip::polyclip(B,A, op = "minus")

  sets <- list("AB" = AB,  "AnoB" = AnoB, "noAB" = noAB)

  data <- data.frame(A=A, B=B)

  venn <- ggplot(data) +
    geom_polygon(mapping = aes(A.x, A.y), color ="black", fill = NA, alpha = 1, size = 0.2) +
    geom_polygon(mapping = aes(B.x, B.y), color ="black", fill = NA, alpha = 1, size = 0.2)

  for(i in 1:length(highlight)){
    set <- highlight[i]
    new_data <- data.frame(set=sets[[set]])
    venn <- venn + geom_polygon(data = new_data, aes(set.x,set.y), color = "black", fill = color[i], alpha = 1, size = 0.2)
  }

  venn <- venn + cowplot::theme_nothing()

  # Add label if desired
  if(!is.null(label)){
    if(label.pos %in% c("bottom.right", "right.bottom")) { lab.x = 1; lab.y = .2 }
    else if(label.pos %in% c("bottom.centre", "centre.bottom", "bottom.center", "center.bottom")) { lab.x = .5; lab.y = .15 }
    else if(label.pos %in% c("bottom.left", "left.bottom")) { lab.x = 0; lab.y = .2 }
    else if(label.pos %in% c("top.right", "right.top")) { lab.x = 1; lab.y = .8 }
    else if(label.pos %in% c("top.centre", "centre.top", "top.center", "center.top")) { lab.x = .5; lab.y = .85 }
    else if(label.pos %in% c("top.left", "left.top")) { lab.x = 0; lab.y = .8 }
    venn <- venn + annotate(geom = "text", label = label, x = lab.x, y = lab.y, hjust = .5, size = label.size, fontface = label.face, color = label.col)
  }

  venn
}


# Highlight areas of 3D Venn
venn3_highlight <- function(highlight = c("ABC", "AnoBnoC"), color = c("red", "pink"),
                            label = NULL, label.pos = "bottom.right", label.face = "italic", label.size = 13, label.col = "black",
                            line.col = "black"){

  # load required packages
  library(polyclip)
  library(VennDiagram)
  library(ggplot2)

  # Create base venn
  invisible(vp <- VennDiagram::draw.triple.venn(area1 = 0, area2 = 0, area3 = 0, n12 = 0, n23 = 0, n13 = 0, n123 = 0,
                                      category = rep("", 3), cex = 0, label.col = NA, scaled = F, fill = NA,
                                      margin = 0, disable.logging = T))

  # Take the circles
  A <- list(list(x = as.vector(vp[[1]][[1]]), y = as.vector(vp[[1]][[2]])))
  B <- list(list(x = as.vector(vp[[2]][[1]]), y = as.vector(vp[[2]][[2]])))
  C <- list(list(x = as.vector(vp[[3]][[1]]), y = as.vector(vp[[3]][[2]])))

  # Find the intersections and other areas
  AB <- polyclip::polyclip(A,B)
  AC <- polyclip::polyclip(A,C)
  BC <- polyclip::polyclip(B,C)

  # Intersection of all
  ABC     <- polyclip::polyclip(A,B) %>% polyclip::polyclip(., C)

  # Intersection of two, subtracting one
  ABnoC   <- polyclip::polyclip(A,B) %>% polyclip::polyclip(., C, op = "minus")
  AnoBC   <- polyclip::polyclip(A,C) %>% polyclip::polyclip(., B, op = "minus")
  noABC   <- polyclip::polyclip(C, B) %>% polyclip::polyclip(., A, op = "minus")

  # Specific of one area
  AnoBnoC <- polyclip::polyclip(A,B, op = "minus") %>% polyclip::polyclip(., C, op = "minus")
  noABnoC <- polyclip::polyclip(B,A, op = "minus") %>% polyclip::polyclip(., C, op = "minus")
  noAnoBC <- polyclip::polyclip(C,A, op = "minus") %>% polyclip::polyclip(., B, op = "minus")

  # Put all intersections in a list
  sets <- list("ABC" = ABC, "ABnoC" = ABnoC, "AnoBC" = AnoBC, "noABC" = noABC, "AnoBnoC" = AnoBnoC, "noABnoC" = noABnoC, "noAnoBC" = noAnoBC)

  # If highlight == "all" set to all clusters
  if(highlight == "all") { highlight <- names(sets); color <- rep(color, 7)}

  # Write a dataframe with the data from each circle
  data <- data.frame(A=A, B=B, C=C)

  # Draw the circles. Line color = black. Fill = NA.
  venn <- ggplot(data) +
    geom_polygon(mapping = aes(A.x, A.y), color = line.col, fill = NA, alpha = 1, size = 0.2) +
    geom_polygon(mapping = aes(B.x, B.y), color = line.col, fill = NA, alpha = 1, size = 0.2) +
    geom_polygon(mapping = aes(C.x, C.y), color = line.col, fill = NA, alpha = 1, size = 0.2)

  # Highlight desired areas by drawing them
  for(i in 1:length(highlight)){
    set <- highlight[i]
    new_data <- data.frame(set=sets[[set]])
    venn <- venn + geom_polygon(data = new_data, aes(set.x,set.y), color = line.col, fill = color[i], alpha = 1, size = 0.2)
  }

  # Remove all the elements from the grid, axes...
  venn <- venn + cowplot::theme_nothing()

  # Add label if desired
  if(!is.null(label)){
    if(label.pos %in% c("bottom.right", "right.bottom")) { lab.x = 1; lab.y = .2 }
    else if(label.pos %in% c("bottom.left", "left.bottom")) { lab.x = 0; lab.y = .2 }
    else if(label.pos %in% c("top.right", "right.top")) { lab.x = 1; lab.y = .9 }
    else if(label.pos %in% c("top.left", "left.top")) { lab.x = 0; lab.y = .9 }
    venn <- venn + annotate(geom = "text", label = label, x = lab.x, y = lab.y, hjust = .5, size = label.size, fontface = label.face, color = label.col)
  }

  # Return venn with shaded areas
  venn
}


# venn3_highlight(highlight = "ABC", color = "black")
#
# venn3_highlight(highlight = c("AnoBC","ABnoC"), color = c("black", "black"))
# venn3_highlight(highlight = c("ABnoC","noABC"), color = c("black", "black"))
# venn3_highlight(highlight = c("AnoBC","noABC"), color = c("black", "black"))
#
# venn3_highlight(highlight = c("AnoBnoC"), color = c("black"))
# venn3_highlight(highlight = c("noABnoC"), color = c("black"))
# venn3_highlight(highlight = c("noAnoBC"), color = c("black"))