venn.diagram: Make a Venn Diagram
In VennDiagram: Generate High-Resolution Venn and Euler Plots
venn.diagram R Documentation
Make a Venn Diagram
Description
This function takes a list and creates a publication-quality TIFF Venn
Diagram
Usage
venn.diagram(x, filename, disable.logging = FALSE, height = 3000,
width = 3000, resolution = 500, imagetype = "tiff",
units = "px", compression = "lzw", na = "stop", main = NULL,
sub = NULL, main.pos = c(0.5, 1.05), main.fontface = "plain",
main.fontfamily = "serif", main.col = "black",
main.cex = 1, main.just = c(0.5, 1), sub.pos = c(0.5,
1.05), sub.fontface = "plain", sub.fontfamily =
"serif", sub.col = "black", sub.cex = 1, sub.just =
c(0.5, 1), category.names = names(x), force.unique =
TRUE, print.mode = "raw", sigdigs = 3, direct.area =
FALSE, area.vector = 0, hyper.test = FALSE, total.population = NULL,
lower.tail = TRUE, ...)
Arguments
x
A list of vectors (e.g., integers, chars), with each component corresponding
to a separate circle in the Venn diagram
filename
Filename for image output, or if NULL returns the grid object itself
disable.logging
Boolean to disable log file output and print to console instead
height
Integer giving the height of the output figure in units
width
Integer giving the width of the output figure in units
resolution
Resolution of the final figure in DPI
imagetype
Specification of the image format (e.g. tiff, png or svg)
units
Size-units to use for the final figure
compression
What compression algorithm should be applied to the final tiff
na
Missing value handling method: "none", "stop", "remove"
main
Character giving the main title of the diagram
sub
Character giving the subtitle of the diagram
main.pos
Vector of length 2 indicating (x,y) of the main title
main.fontface
Character giving the fontface (font style) of the main title
main.fontfamily
Character giving the fontfamily (font type) of the main title
main.col
Character giving the colour of the main title
main.cex
Number giving the cex (font size) of the main title
main.just
Vector of length 2 indicating horizontal and vertical justification
of the main title
sub.pos
Vector of length 2 indicating (x,y) of the subtitle
sub.fontface
Character giving the fontface (font style) of the subtitle
sub.fontfamily
Character giving the fontfamily (font type) of the subtitle
sub.col
Character Colour of the subtitle
sub.cex
Number giving the cex (font size) of the subtitle
sub.just
Vector of length 2 indicating horizontal and vertical justification of
the subtitle
category.names
Allow specification of category names using plotmath syntax
force.unique
Logical specifying whether to use only unique elements in each item
of the input list or use all elements. Defaults to FALSE
print.mode
Can be either 'raw' or 'percent'. This is the format that the numbers will be printed in. Can pass in a vector with the second element being printed under the first
sigdigs
If one of the elements in print.mode is 'percent', then this is how many significant digits will be kept
direct.area
If this is equal to true, then the vector passed into area.vector will be directly assigned to the areas of the corresponding regions. Only use this if you know which positions in the vector correspond to which regions in the diagram
area.vector
An argument to be used when direct.area is true. These are the areas of the corresponding regions in the Venn Diagram
hyper.test
If there are only two categories in the venn diagram and total.population is not NULL, then perform the hypergeometric test and add it to the sub title.
total.population
An argument to be used when hyper.test is true. This is the total population size
lower.tail
logical; if TRUE (default), probabilities are P[X <= x], otherwise, P[X > x]
...
A series of graphical parameters tweaking the plot. See below for details
Details
Argument Venn Sizes Class
Description
lwd 1,2,3,4,5 numeric
Vector giving the width of each circle's circumference
lty 1,2,3,4,5 numeric
Vector giving the dash pattern of each circle's circumference
col 1,2,3,4,5 character
Vector giving the colour of each circle's circumference
fill 1,2,3,4,5 character
Vector giving the colour of each circle's area
alpha 1,2,3,4,5 numeric
Vector giving the alpha transparency of each circle's area
label.col 1,2,3,4,5 character
Vector giving the colour for each area label (length =
1/3/7/15 based on set-number)
cex 1,2,3,4,5 numeric
Vector giving the size for each area label (length =
1/3/7/15 based on set-number)
fontface 1,2,3,4,5 character
Vector giving the fontface for each area label (length =
1/3/7/15 based on set-number)
fontfamily 1,2,3,4,5 character
Vector giving the fontfamily for each area label (length =
1/3/7/15 based on set-number)
cat.pos 1,2,3,4,5 numeric
Vector giving the position (in degrees) of each category
name along the circle, with 0 at 12 o'clock
cat.dist 1,2,3,4,5 numeric
Vector giving the distance (in npc units) of each category
name from the edge of the circle (can be negative)
cat.cex 1,2,3,4,5 numeric
Vector giving the size for each category name
cat.col 1,2,3,4,5 character
Vector giving the colour for each category name
cat.fontface 1,2,3,4,5 character
Vector giving the fontface for each category name
cat.fontfamily 1,2,3,4,5 character
Vector giving the fontfamily for each category name
cat.just 1,2,3,4,5 numeric
List (length = 1/2/3/4 based on set number) of Vectors
of length 2 indicating horizontal and vertical justification
for each category name
cat.default.pos 1,2,3 character
One of c('outer', 'text') to specify the default location
of category names (cat.pos and cat.dist are handled differently)
cat.prompts 2 numeric
Boolean indicating whether to display help text on category
name positioning or not
margin 1,2,3,4,5 numeric
Number giving the amount of whitespace around the diagram
in grid units
rotation.degree 1,2,3,4,5 numeric
Number of degrees to rotate the entire diagram
rotation.centre 1,2,3,4,5 numeric
Vector of length 2 indicating (x,y) of the rotation
centre
rotation 3 numeric
Number giving the clockwise rotation of a three-set Venn
diagram (1, 2, or 3)
reverse 3 logical
Reflect the three-set Venn diagram along its central
vertical axis of symmetry. Use in combination with rotation
to generate all possible set orders
euler.d 2, 3 logical
Enable Euler diagrams for two-set and three-set Venn
diagrams (Venn Diagrams with moveable circles)
scaled 2, 3 logical
Enable scaling for two-set and certain three-set Euler
diagrams. (euler.d must be true to enable this)
sep.dist 2, 3 numeric
Controls the separation between distinct circles in
certain two-set or three-set Euler diagrams.
offset 2, 3 numeric
Number between 0 and 1 giving the amount to offset the
smaller circle by in the inclusion type of two-set Euler
diagram and certain similar three-set Euler diagrams.
inverted 2 logical
Flip the two-set Venn diagram along its vertical
axis (distinguished from reverse)
ext.text 2 logical
Allow external text labels when areas are small
ext.percent 2 numeric
A vector (length 3) indicating the proportion that
a partial area has to be smaller than to trigger externa
l text placement. The elements allow for individual
control of the areas in the order of the first area,
second area and intersection area.
ext.pos 2 numeric
A vector (length 1 or 2) giving the positions (in degrees)
of the external area labels along the
circles, with 0 (default) at 12 o'clock
ext.line.lwd 2 numeric
Width of line connecting to ext.text
ext.line.lty 2 numeric
The dash pattern of the lines connecting the external
area labels to their anchor points.
ext.dist 2 numeric
Vector of length 1 or 2 indicating length of external
line (use negative values to shorten the line )
ext.length 2 numeric
Vector of length 1 or 2 indicating the proportion of
the external line that is drawn from the anchor to the text
Value
Plots a figure to the file given by the filename argument.
Author(s)
Hanbo Chen
See Also
draw.single.venn, draw.pairwise.venn,
draw.triple.venn, draw.quad.venn,
draw.quintuple.venn
Examples
# Note: most examples are listed as dontrun to meet CRAN requirements,
# but all should work as-is!
# compact and minimal notation
## Not run:
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'
)
);
## End(Not run)
# 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
);
## Not run:
# 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
);
## End(Not run)
# 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
);
## Not run:
# 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();
## End(Not run)
#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.
## Not run:
# 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
## End(Not run)
VennDiagram documentation built on April 13, 2022, 1:06 a.m.
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| venn.diagram | R Documentation |
Make a Venn Diagram
Description
This function takes a list and creates a publication-quality TIFF Venn Diagram
Usage
venn.diagram(x, filename, disable.logging = FALSE, height = 3000,
width = 3000, resolution = 500, imagetype = "tiff",
units = "px", compression = "lzw", na = "stop", main = NULL,
sub = NULL, main.pos = c(0.5, 1.05), main.fontface = "plain",
main.fontfamily = "serif", main.col = "black",
main.cex = 1, main.just = c(0.5, 1), sub.pos = c(0.5,
1.05), sub.fontface = "plain", sub.fontfamily =
"serif", sub.col = "black", sub.cex = 1, sub.just =
c(0.5, 1), category.names = names(x), force.unique =
TRUE, print.mode = "raw", sigdigs = 3, direct.area =
FALSE, area.vector = 0, hyper.test = FALSE, total.population = NULL,
lower.tail = TRUE, ...)
Arguments
x |
A list of vectors (e.g., integers, chars), with each component corresponding to a separate circle in the Venn diagram |
filename |
Filename for image output, or if NULL returns the grid object itself |
disable.logging |
Boolean to disable log file output and print to console instead |
height |
Integer giving the height of the output figure in units |
width |
Integer giving the width of the output figure in units |
resolution |
Resolution of the final figure in DPI |
imagetype |
Specification of the image format (e.g. tiff, png or svg) |
units |
Size-units to use for the final figure |
compression |
What compression algorithm should be applied to the final tiff |
na |
Missing value handling method: "none", "stop", "remove" |
main |
Character giving the main title of the diagram |
sub |
Character giving the subtitle of the diagram |
main.pos |
Vector of length 2 indicating (x,y) of the main title |
main.fontface |
Character giving the fontface (font style) of the main title |
main.fontfamily |
Character giving the fontfamily (font type) of the main title |
main.col |
Character giving the colour of the main title |
main.cex |
Number giving the cex (font size) of the main title |
main.just |
Vector of length 2 indicating horizontal and vertical justification of the main title |
sub.pos |
Vector of length 2 indicating (x,y) of the subtitle |
sub.fontface |
Character giving the fontface (font style) of the subtitle |
sub.fontfamily |
Character giving the fontfamily (font type) of the subtitle |
sub.col |
Character Colour of the subtitle |
sub.cex |
Number giving the cex (font size) of the subtitle |
sub.just |
Vector of length 2 indicating horizontal and vertical justification of the subtitle |
category.names |
Allow specification of category names using plotmath syntax |
force.unique |
Logical specifying whether to use only unique elements in each item of the input list or use all elements. Defaults to FALSE |
print.mode |
Can be either 'raw' or 'percent'. This is the format that the numbers will be printed in. Can pass in a vector with the second element being printed under the first |
sigdigs |
If one of the elements in print.mode is 'percent', then this is how many significant digits will be kept |
direct.area |
If this is equal to true, then the vector passed into area.vector will be directly assigned to the areas of the corresponding regions. Only use this if you know which positions in the vector correspond to which regions in the diagram |
area.vector |
An argument to be used when direct.area is true. These are the areas of the corresponding regions in the Venn Diagram |
hyper.test |
If there are only two categories in the venn diagram and total.population is not NULL, then perform the hypergeometric test and add it to the sub title. |
total.population |
An argument to be used when hyper.test is true. This is the total population size |
lower.tail |
logical; if TRUE (default), probabilities are P[X <= x], otherwise, P[X > x] |
... |
A series of graphical parameters tweaking the plot. See below for details |
Details
| Argument | Venn Sizes | Class | Description |
lwd | 1,2,3,4,5 | numeric | Vector giving the width of each circle's circumference |
lty | 1,2,3,4,5 | numeric | Vector giving the dash pattern of each circle's circumference |
col | 1,2,3,4,5 | character | Vector giving the colour of each circle's circumference |
fill | 1,2,3,4,5 | character | Vector giving the colour of each circle's area |
alpha | 1,2,3,4,5 | numeric | Vector giving the alpha transparency of each circle's area |
label.col | 1,2,3,4,5 | character | Vector giving the colour for each area label (length = |
| 1/3/7/15 based on set-number) | |||
cex | 1,2,3,4,5 | numeric | Vector giving the size for each area label (length = |
| 1/3/7/15 based on set-number) | |||
fontface | 1,2,3,4,5 | character | Vector giving the fontface for each area label (length = |
| 1/3/7/15 based on set-number) | |||
fontfamily | 1,2,3,4,5 | character | Vector giving the fontfamily for each area label (length = |
| 1/3/7/15 based on set-number) | |||
cat.pos | 1,2,3,4,5 | numeric | Vector giving the position (in degrees) of each category |
| name along the circle, with 0 at 12 o'clock | |||
cat.dist | 1,2,3,4,5 | numeric | Vector giving the distance (in npc units) of each category |
| name from the edge of the circle (can be negative) | |||
cat.cex | 1,2,3,4,5 | numeric | Vector giving the size for each category name |
cat.col | 1,2,3,4,5 | character | Vector giving the colour for each category name |
cat.fontface | 1,2,3,4,5 | character | Vector giving the fontface for each category name |
cat.fontfamily | 1,2,3,4,5 | character | Vector giving the fontfamily for each category name |
cat.just | 1,2,3,4,5 | numeric | List (length = 1/2/3/4 based on set number) of Vectors |
| of length 2 indicating horizontal and vertical justification | |||
| for each category name | |||
cat.default.pos | 1,2,3 | character | One of c('outer', 'text') to specify the default location |
| of category names (cat.pos and cat.dist are handled differently) | |||
cat.prompts | 2 | numeric | Boolean indicating whether to display help text on category |
| name positioning or not | |||
margin | 1,2,3,4,5 | numeric | Number giving the amount of whitespace around the diagram |
| in grid units | |||
rotation.degree | 1,2,3,4,5 | numeric | Number of degrees to rotate the entire diagram |
rotation.centre | 1,2,3,4,5 | numeric | Vector of length 2 indicating (x,y) of the rotation |
| centre | |||
rotation | 3 | numeric | Number giving the clockwise rotation of a three-set Venn |
| diagram (1, 2, or 3) | |||
reverse | 3 | logical | Reflect the three-set Venn diagram along its central |
vertical axis of symmetry. Use in combination with rotation |
|||
| to generate all possible set orders | |||
euler.d | 2, 3 | logical | Enable Euler diagrams for two-set and three-set Venn |
| diagrams (Venn Diagrams with moveable circles) | |||
scaled | 2, 3 | logical | Enable scaling for two-set and certain three-set Euler |
| diagrams. (euler.d must be true to enable this) | |||
sep.dist | 2, 3 | numeric | Controls the separation between distinct circles in |
| certain two-set or three-set Euler diagrams. | |||
offset | 2, 3 | numeric | Number between 0 and 1 giving the amount to offset the |
| smaller circle by in the inclusion type of two-set Euler | |||
| diagram and certain similar three-set Euler diagrams. | |||
inverted | 2 | logical | Flip the two-set Venn diagram along its vertical |
axis (distinguished from reverse) |
|||
ext.text | 2 | logical | Allow external text labels when areas are small |
ext.percent | 2 | numeric | A vector (length 3) indicating the proportion that |
| a partial area has to be smaller than to trigger externa | |||
| l text placement. The elements allow for individual | |||
| control of the areas in the order of the first area, | |||
| second area and intersection area. | |||
ext.pos | 2 | numeric | A vector (length 1 or 2) giving the positions (in degrees) |
| of the external area labels along the | |||
| circles, with 0 (default) at 12 o'clock | |||
ext.line.lwd | 2 | numeric | Width of line connecting to ext.text |
ext.line.lty | 2 | numeric | The dash pattern of the lines connecting the external |
| area labels to their anchor points. | |||
ext.dist | 2 | numeric | Vector of length 1 or 2 indicating length of external |
| line (use negative values to shorten the line ) | |||
ext.length | 2 | numeric | Vector of length 1 or 2 indicating the proportion of |
| the external line that is drawn from the anchor to the text | |||
Value
Plots a figure to the file given by the filename argument.
Author(s)
Hanbo Chen
See Also
draw.single.venn, draw.pairwise.venn,
draw.triple.venn, draw.quad.venn,
draw.quintuple.venn
Examples
# Note: most examples are listed as dontrun to meet CRAN requirements,
# but all should work as-is!
# compact and minimal notation
## Not run:
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'
)
);
## End(Not run)
# 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
);
## Not run:
# 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
);
## End(Not run)
# 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
);
## Not run:
# 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();
## End(Not run)
#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.
## Not run:
# 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
## End(Not run)
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