# Note: most examples are listed as dontrun to meet CRAN requirements,
# but all should work as-is!
# compact and minimal notation
if (FALSE) {
venn.plot <- venn.diagram(
list(A = 1:150, B = 121:170),
filename = tempfile(
pattern = 'Venn_2set_simple',
fileext = '.tiff'
)
);
venn.plot <- venn.diagram(
list(A = 1:150, B = 121:170, C = 101:200),
filename = tempfile(
pattern = 'Venn_3set_simple',
fileext = '.tiff'
)
);
}
# a more elaborate two-set Venn diagram with title and subtitle
venn.plot <- venn.diagram(
x = list(
"A" = 1:100,
"B" = 96:140
),
filename = tempfile(
pattern = 'Venn_2set_complex',
fileext = '.tiff'
),
scaled = TRUE,
ext.text = TRUE,
ext.line.lwd = 2,
ext.dist = -0.15,
ext.length = 0.9,
ext.pos = -4,
inverted = TRUE,
cex = 2.5,
cat.cex = 2.5,
rotation.degree = 45,
main = "Complex Venn Diagram",
sub = "Featuring: rotation and external lines",
main.cex = 2,
sub.cex = 1
);
if (FALSE) {
# sample three-set Euler diagram
venn.plot <- venn.diagram(
x = list(
"Num A" = paste("Num", 1:100),
"Num B" = c(paste("Num", 61:70), paste("Num", 71:100)),
"Num C" = c(paste("Num", 41:60), paste("Num", 61:70))),
euler.d = TRUE,
filename = tempfile(
pattern = 'Euler_3set_simple',
fileext = '.tiff'
),
cat.pos = c(-20, 0, 20),
cat.dist = c(0.05, 0.05, 0.02),
cex = 2.5,
cat.cex = 2.5,
reverse = TRUE
);
# sample three-set Euler diagram
venn.plot <- venn.diagram(
x = list(
A = c(1:10),
B = c(11:90),
C = c(81:90)
),
euler.d = TRUE,
filename = tempfile(
pattern = 'Euler_3set_scaled',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.pos = 0
);
}
# sample four-set Venn Diagram
A <- sample(1:1000, 400, replace = FALSE);
B <- sample(1:1000, 600, replace = FALSE);
C <- sample(1:1000, 350, replace = FALSE);
D <- sample(1:1000, 550, replace = FALSE);
E <- sample(1:1000, 375, replace = FALSE);
venn.plot <- venn.diagram(
x = list(
A = A,
D = D,
B = B,
C = C
),
filename = tempfile(
pattern = 'Venn_4set_pretty',
fileext = '.tiff'
),
col = "transparent",
fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),
alpha = 0.50,
label.col = c("orange", "white", "darkorchid4", "white",
"white", "white", "white", "white", "darkblue", "white",
"white", "white", "white", "darkgreen", "white"),
cex = 1.5,
fontfamily = "serif",
fontface = "bold",
cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),
cat.cex = 1.5,
cat.pos = 0,
cat.dist = 0.07,
cat.fontfamily = "serif",
rotation.degree = 270,
margin = 0.2
);
# sample five-set Venn Diagram
venn.plot <- venn.diagram(
x = list(
A = A,
B = B,
C = C,
D = D,
E = E
),
filename = tempfile(
pattern = 'Venn_5set_pretty',
fileext = '.tiff'
),
col = "black",
fill = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
alpha = 0.50,
cex = c(1.5, 1.5, 1.5, 1.5, 1.5, 1, 0.8, 1, 0.8, 1, 0.8, 1, 0.8,
1, 0.8, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 1, 1, 1, 1, 1.5),
cat.col = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
cat.cex = 1.5,
cat.fontface = "bold",
margin = 0.05
);
# Complex three-way Venn with labels & sub-/super-scripts
venn.plot <- venn.diagram(
x = list(
I = c(1:60, 61:105, 106:140, 141:160, 166:175, 176:180, 181:205,
206:220),
II = c(531:605, 476:530, 336:375, 376:405, 181:205, 206:220, 166:175,
176:180),
III = c(61:105, 106:140, 181:205, 206:220, 221:285, 286:335, 336:375,
376:405)
),
category.names = c(
expression( bold('A'['1: subscript']) ),
expression( bold('B'^'2: going up') ),
expression( paste(bold('C'^'3'), bold('X'['i' <= 'r'^'2']^'2') ) )
),
filename = tempfile(
pattern = 'Fig3-1_triple_labels_sub_and_superscripts',
fileext = '.tiff'
),
output = TRUE,
height = 3000,
width = 3000,
resolution = 300,
compression = 'lzw',
units = 'px',
lwd = 6,
lty = 'blank',
fill = c('yellow', 'purple', 'green'),
cex = 3.5,
fontface = "bold",
fontfamily = "sans",
cat.cex = 3,
cat.fontface = "bold",
cat.default.pos = "outer",
cat.pos = c(-27, 27, 135),
cat.dist = c(0.055, 0.055, 0.085),
cat.fontfamily = "sans",
rotation = 1
);
# Complex 3-way Venn using expressions
venn.plot <- venn.diagram(
x = list(
"Num A" = paste("Num", 1:100),
"Num B" = c(paste("Num", 61:70), paste("Num", 71:100)),
"Num C" = c(paste("Num", 41:60), paste("Num", 61:70))),
category.names = c(
expression( bold('A'['1']) ),
expression( bold('A'['2']) ),
expression( bold('A'['3']) )
),
euler.d = TRUE,
filename = tempfile(
pattern = 'Fig3-2_Euler_3set_simple_with_subscripts',
fileext = '.tiff'
),
cat.pos = c(-20, 0, 20),
cat.dist = c(0.05, 0.05, 0.02),
cex = 2.5,
cat.cex = 2.5,
reverse = TRUE
);
if (FALSE) {
# Example to print to screen
venn.plot <- venn.diagram(
x = list(
sample1 = c(1:40),
sample2 = c(30:60)
),
filename = NULL,
disable.logging = TRUE
);
# Save picture to non-TIFF file type
# currently working on adding this functionality directly into venn.diagram
venn.plot <- venn.diagram(
x = list (
A = 1:10,
B = 6:25
),
filename = NULL,
disable.logging = TRUE
);
jpeg(tempfile(pattern = 'venn_jpeg', fileext = '.jpg'));
grid.draw(venn.plot);
dev.off();
}
#dontrun-starts-here
### NB: All figures from the paper can be run, but are turned off from
### automatic execution to reduce burden on CRAN computing resources.
if (FALSE) {
# Figure 1A
venn.plot <- venn.diagram(
x = list(
Label = 1:100
),
filename = tempfile(
pattern = '1A-single_Venn',
fileext = '.tiff'
),
col = "black",
lwd = 9,
fontface = "bold",
fill = "grey",
alpha = 0.75,
cex = 4,
cat.cex = 3,
cat.fontface = "bold",
);
# Figure 1B
venn.plot <- venn.diagram(
x = list(
X = 1:150,
Y = 121:180
),
filename = tempfile(
pattern = '1B-double_Venn',
fileext = '.tiff'
),
lwd = 4,
fill = c("cornflowerblue", "darkorchid1"),
alpha = 0.75,
label.col = "white",
cex = 4,
fontfamily = "serif",
fontface = "bold",
cat.col = c("cornflowerblue", "darkorchid1"),
cat.cex = 3,
cat.fontfamily = "serif",
cat.fontface = "bold",
cat.dist = c(0.03, 0.03),
cat.pos = c(-20, 14)
);
# Figure 1C
venn.plot <- venn.diagram(
x = list(
R = c(1:70, 71:110, 111:120, 121:140),
B = c(141:200, 71:110, 111:120, 201:230),
G = c(231:280, 111:120, 121:140, 201:230)
),
filename = tempfile(
pattern = '1C-triple_Venn',
fileext = '.tiff'
),
col = "transparent",
fill = c("red", "blue", "green"),
alpha = 0.5,
label.col = c("darkred", "white", "darkblue", "white",
"white", "white", "darkgreen"),
cex = 2.5,
fontfamily = "serif",
fontface = "bold",
cat.default.pos = "text",
cat.col = c("darkred", "darkblue", "darkgreen"),
cat.cex = 2.5,
cat.fontfamily = "serif",
cat.dist = c(0.06, 0.06, 0.03),
cat.pos = 0
);
# Figure 1D
venn.plot <- venn.diagram(
x = list(
I = c(1:60, 61:105, 106:140, 141:160, 166:175, 176:180, 181:205,
206:220),
IV = c(531:605, 476:530, 336:375, 376:405, 181:205, 206:220, 166:175,
176:180),
II = c(61:105, 106:140, 181:205, 206:220, 221:285, 286:335, 336:375,
376:405),
III = c(406:475, 286:335, 106:140, 141:160, 166:175, 181:205, 336:375,
476:530)
),
filename = tempfile(
pattern = '1D-quadruple_Venn',
fileext = '.tiff'
),
col = "black",
lty = "dotted",
lwd = 4,
fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),
alpha = 0.50,
label.col = c("orange", "white", "darkorchid4", "white", "white", "white",
"white", "white", "darkblue", "white",
"white", "white", "white", "darkgreen", "white"),
cex = 2.5,
fontfamily = "serif",
fontface = "bold",
cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),
cat.cex = 2.5,
cat.fontfamily = "serif"
);
# Figure 2-1
venn.plot <- venn.diagram(
x = list(
A = 1:105,
B = 101:115
),
filename = tempfile(
pattern = '2-1_special_case_ext-text',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.pos = c(-20, 20),
ext.line.lty = "dotted",
ext.line.lwd = 2,
ext.pos = 12,
ext.dist = -0.12,
ext.length = 0.85
);
# Figure 2-2
venn.plot <- venn.diagram(
x = list(
A = 1:100,
B = 1:10
),
filename = tempfile(
pattern = '2-2_special_case_pairwise-inclusion',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.pos = 0
);
# Figure 2-3
venn.plot <- venn.diagram(
x = list(
A = 1:150,
B = 151:250
),
filename = tempfile(
pattern = '2-3_special_case_pairwise-exclusion',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.pos = c(0, 0),
cat.dist = 0.05
);
# Figure 2-4
venn.plot <- venn.diagram(
x = list(
A = c(1:50, 101:140, 141:160, 161:170),
B = c(171:230, 101:140, 161:170, 291:320),
C = c(141:160, 161:170, 291:320)
),
filename = tempfile(
pattern = '2-4_triple_special_case-001',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.dist = c(0.05, 0.05, -0.1)
);
# Figure 2-5
venn.plot <- venn.diagram(
x = list(
A = c(1:100),
B = c(61:70, 71:100),
C = c(41:60, 61:70)
),
filename = tempfile(
pattern = '2-5_triple_special_case-012AA',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.pos = c(-25, 0, 30),
cat.dist = c(0.05, 0.05, 0.02)
);
# Figure 2-6
venn.plot <- venn.diagram(
x = list(
A = c(1:90),
B = c(1:25),
C = c(1:5)
),
filename = tempfile(
pattern = '2-6_triple_special_case-022AAAO',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.pos = 0,
cat.dist = c(0.03, 0.03, 0.01)
);
# Figure 2-7
venn.plot <- venn.diagram(
x = list(
A = c(1:20),
B = c(21:80),
C = c(81:210)
),
filename = tempfile(
pattern = '2-7_triple_special_case-100',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.dist = 0.05
);
# Figure 2-8
venn.plot <- venn.diagram(
x = list(
A = c(1:80),
B = c(41:150),
C = c(71:100)
),
filename = tempfile(
pattern = '2-8_triple_special_case-011A',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.dist = c(0.07, 0.07, 0.02),
cat.pos = c(-20, 20, 20)
);
# Figure 2-9
venn.plot <- venn.diagram(
x = list(
A = c(1:10),
B = c(11:90),
C = c(81:90)
),
filename = tempfile(
pattern = '2-9_triple_special_case-121AO',
fileext = '.tiff'
),
cex = 2.5,
cat.cex = 2.5,
cat.pos = 0,
cat.dist = c(0.04, 0.04, 0.02),
reverse = TRUE
);
#dontrun-ends-here
}
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