The venndir package provides Venn directional diagrams, that can optionally display item labels inside the overlap regions.
The pkgdown reference: jmw86069.github.io/venndir
Installation
The development version of venndir can be installed with:
# install.packages("remotes")
remotes::install_github("jmw86069/venndir");Features of venndir
The core is venndir() which takes a setlist as input and produces a Venn diagram. When the setlist contains directionality (sign), the directional overlaps are also displayed.
To illustrate the point, make_venn_test() is used to create test setlist data.
# silence the GEOS warnings
options("warn"=-1)
library(venndir)
setlist <- make_venn_test(100, 3)
setlist
#> $set_A
#> [1] "item_067" "item_042" "item_050" "item_043" "item_014" "item_025"
#> [7] "item_090" "item_091" "item_069" "item_093" "item_057" "item_009"
#> [13] "item_072" "item_026" "item_007" "item_099" "item_089" "item_083"
#> [19] "item_036" "item_078" "item_097" "item_076" "item_015" "item_032"
#> [25] "item_086" "item_084" "item_041" "item_023" "item_027" "item_060"
#> [31] "item_053" "item_079"
#>
#> $set_B
#> [1] "item_053" "item_027" "item_096" "item_038" "item_089" "item_034"
#> [7] "item_093" "item_069" "item_072" "item_076" "item_063" "item_013"
#> [13] "item_082" "item_025" "item_097" "item_021"
#>
#> $set_C
#> [1] "item_079" "item_041" "item_047" "item_090" "item_060" "item_095"
#> [7] "item_016" "item_006" "item_072" "item_086" "item_091" "item_039"
#> [13] "item_031" "item_081" "item_050"A setlist is a list of vectors. The names of the list, one for each vector, are the set names. Each vector contains items which are the subject of the Venn overlaps.
Given a setlist, you can create a Venn diagram with venndir():
venndir(setlist)
You can make a proportional Venn diagram, also known as a Euler diagram. More examples of proportional Venn diagrams are described below, but for now the simplest approach is to add argument proportional=TRUE:
venndir(setlist,
overlap_type="overlap",
proportional=TRUE)
The default output use base R graphics, but you can use ggplot2 with the argument plot_style="gg":
venndir(setlist,
overlap_type="overlap",
proportional=TRUE,
plot_style="gg")
Finally, you can add a legend with venndir_legender():
vo <- venndir(setlist,
proportional=TRUE,
overlap_type="overlap",
show_segments=FALSE,
plot_style="gg")
venndir_legender(setlist=setlist, venndir_out=vo, font_cex=0.8)
The function invisibly returns the ggplot object which can be manipulated alongside other grid graphical objects.
Venn Direction
For a more interesting case, make_venn_test(..., do_signed=TRUE) creates a setlist with directionality (sign), which means each item is associated with a numerical direction:
-
+1for up -
-1for down
In this case, each vector in the setlist is a named vector, whose names are the items, and whose values are the signed direction +1 or -1. Take a look.
setlist_dir <- make_venn_test(100, 3, do_signed=TRUE)
setlist_dir
#> $set_A
#> item_067 item_042 item_050 item_043 item_014 item_025 item_090 item_091
#> -1 1 1 -1 -1 1 -1 -1
#> item_069 item_093 item_057 item_009 item_072 item_026 item_007 item_099
#> -1 1 1 -1 1 1 -1 -1
#> item_089 item_083 item_036 item_078 item_097 item_076 item_015 item_032
#> -1 1 1 1 1 1 -1 1
#> item_086 item_084 item_041 item_023 item_027 item_060 item_053 item_079
#> 1 1 -1 1 -1 1 1 -1
#>
#> $set_B
#> item_053 item_027 item_096 item_038 item_089 item_034 item_093 item_069
#> 1 -1 1 -1 -1 -1 1 -1
#> item_072 item_076 item_063 item_013 item_082 item_025 item_097 item_021
#> 1 1 1 1 1 -1 -1 -1
#>
#> $set_C
#> item_079 item_041 item_047 item_090 item_060 item_095 item_016 item_006
#> -1 -1 1 -1 1 1 1 -1
#> item_072 item_086 item_091 item_039 item_031 item_081 item_050
#> 1 1 1 1 -1 1 -1For biological data, direction is important and relevant. Whether a gene is regulated up or down might be the difference between disease and treatment.
Note
make_venn_tests()can simulate concordance, and the default isconcordance=0.5. Concordance is a measure of how frequently two directions are the same, and is defined(agree - disagree) / (n). Thus,concordance=0means there are the same number that agree as disagree in direction, andconcordance=1means every element agrees in direction.
There are a few ways to summarize directional overlaps, which vary by the amount of detail.
-
overlap_type="overlap"- This method ignores direction. -
overlap_type="agreement"- This method displays agreement and disagreement, with no details about up/down direction. -
overlap_type="concordance"- (default) This method displays concordant directions, up-up, down-down; all discordant combinations are grouped together as “discordant”. -
overlap_type="each"- This method displays each directional overlap.
overlap_type=“concordance”
Let’s start with overlap_type="concordance" which displays the number up-up, and the number down-down, and everything else is considered “discordant”. This approach is effective at conveying direction, without too many unhelpful details.
venndir(setlist_dir)
It is mostly helpful when you want to see how many overlaps agree up and down, and when the overlaps that disagree in direction are less interesting. For example, sometimes the overlaps are mostly up-up and rarely down-down, which can be very helpful to know.
overlap_type=“each”
The option overlap_type="each" shows the count for each directional combination. It works best when you want to see all the details, typically for only 2 or 3 sets.
venndir(setlist_dir, overlap_type="each")
overlap_type=“agreement”
The option overlap_type="agreement" shows the count for each overlap that agrees in direction, regardless of the direction; and the count for overlaps that disagree in direction.
This option is especially good at summarizing the number that agree and disagree, without including potentially confusing details.
venndir(setlist_dir, overlap_type="agreement")
overlap_type=“overlap”
The option overlap_type="overlap" simply ignores directionality.
venndir(setlist_dir, overlap_type="overlap")
Proportional Venn Direction
As shown above, you can switch output to a proportional Venn diagram, which uses the really nice eulerr R package.
vo <- venndir(setlist_dir,
proportional=TRUE,
font_cex=c(1.3, 0.9, 0.7))
venndir_legender(setlist_dir, venndir_out=vo, x="bottomright", font_cex=0.6)
Labeling is often a challenge with proportional Venn diagrams. By default, for directional Venn counts, if a polygon is less than 5% of the total area, the label is placed outside. For standard Venn counts the default threshold is 1%.
Below is the same diagram, showing only the overlap counts, and not the directional counts.
You can change the threshold for placing labels outside with the argument inside_percent_threshold, which takes integer percent values from 0 to 100.
venndir(setlist,
proportional=TRUE,
inside_percent_threshold=0.1,
overlap_type="overlap",
font_cex=c(1.3, 1))
Customizing the Venn diagram
The output of venndir() is a list with:
-
"venn_spdf"- which contains polygon coordinates stored as asp::SpatialPolygonsDataFrame. Essentially it stores each Venn polygon, with annotations in adata.frame. -
"label_df"- adata.framewith individual text labels, colors, and coordinates.
You can edit the label_df data manually, as needed, then render the Venn diagram using render_venndir(). (I really like having a function named render_venndir()…)
setlist <- make_venn_test(1000, 3, do_signed=FALSE)
vo <- venndir(setlist, proportional=TRUE, do_plot=FALSE);
print(head(vo$label_df));
#> x y text venn_counts overlap_set type x_offset y_offset
#> set_A -8.730 -1.53 31 31 set_A main -3.516 -0.998
#> set_B 8.855 -4.38 390 390 set_B main 9.603 -3.716
#> set_C -4.662 9.95 71 71 set_C main -0.888 4.745
#> set_A&set_B -4.140 -2.24 27 27 set_A&set_B main 0.000 0.000
#> set_A&set_C -6.591 2.59 6 6 set_A&set_C main -3.353 1.592
#> set_B&set_C 0.117 4.73 76 76 set_B&set_C main 0.000 0.000
#> show_label vjust hjust halign rot color fontsize border lty lwd
#> set_A NA 0.5 0.5 0.5 0 #262626FF 14 NA 1 1
#> set_B NA 0.5 0.5 0.5 0 #262626FF 14 NA 1 1
#> set_C NA 0.5 0.5 0.5 0 #262626FF 14 NA 1 1
#> set_A&set_B NA 0.5 0.5 0.5 0 #262626FF 14 NA 1 1
#> set_A&set_C NA 0.5 0.5 0.5 0 #262626FF 14 NA 1 1
#> set_B&set_C NA 0.5 0.5 0.5 0 #262626FF 14 NA 1 1
#> fill padding padding_unit r r_unit overlap_sign items
#> set_A NA 3 pt 3 pt set_A|1 0 0 item_052....
#> set_B NA 3 pt 3 pt set_B|0 1 0 item_011....
#> set_C NA 3 pt 3 pt set_C|0 0 1 item_059....
#> set_A&set_B NA 3 pt 3 pt set_A&set_B|1 1 0 item_019....
#> set_A&set_C NA 3 pt 3 pt set_A&set_C|1 0 1 item_093....
#> set_B&set_C NA 3 pt 3 pt set_B&set_C|0 1 1 item_060....
#> nsets main_venn_counts overlap set_is_hidden show_items count
#> set_A 1 31 outside FALSE none inside
#> set_B 1 390 outside FALSE none inside
#> set_C 1 71 outside FALSE none inside
#> set_A&set_B 2 27 none FALSE none inside
#> set_A&set_C 2 6 none FALSE none outside
#> set_B&set_C 2 76 none FALSE none inside
#> label_left_outside label_left_inside label_right_outside
#> set_A TRUE TRUE FALSE
#> set_B TRUE TRUE FALSE
#> set_C TRUE TRUE FALSE
#> set_A&set_B FALSE TRUE FALSE
#> set_A&set_C TRUE FALSE FALSE
#> set_B&set_C FALSE TRUE FALSE
#> label_right_inside hjust_outside hjust_inside vjust_outside
#> set_A FALSE 0.5 0.5 0.5
#> set_B FALSE 0.5 0.5 0.5
#> set_C FALSE 0.5 0.5 0.5
#> set_A&set_B FALSE 0.5 0.5 0.5
#> set_A&set_C FALSE 1.0 0.5 0.0
#> set_B&set_C FALSE 0.5 0.5 0.5
#> vjust_inside
#> set_A 0.5
#> set_B 0.5
#> set_C 0.5
#> set_A&set_B 0.5
#> set_A&set_C 0.5
#> set_B&set_C 0.5
vo$label_df[1:3,"border"] <- c("red4", "darkorange", "blue4");
vo$label_df[1:3,"fill"] <- c("red3", "darkorange2", "blue3");
render_venndir(vo);
A convenience function venndir_label_style() is provided which provides two features:
- It can adjust a label positions and visibility using
label_preset. - It can adjust label visual style using
label_style.
venndir_label_style() and label_preset
The label_preset has a few pre-configured options:
-
"main inside"- displays main set labels, and counts inside each polygon. -
"main outside"- displays each set label outside, and counts inside. -
"outside"- displays set labels and counts outside. -
"main items"- displays set names outside, and item labels inside each polygon. See below for examples.
vo4 <- venndir_label_style(vo,
label_preset="main outside",
inside_percent_threshold=0)
render_venndir(vo4);
You can hide line segments with show_segments=FALSE.
vo4l <- venndir_label_style(vo,
label_preset="main outside",
inside_percent_threshold=0)
render_venndir(vo4l,
show_segments=FALSE);
venndir_label_style() and label_style
The label_style is used for visual effects, to improve visibility of the text labels. It applies two basic operations, fill and border.
Fill options:
-
"basic"- removes background fill -
"shaded"- partial transparent fill using the overlap color -
"fill"- fill using the overlap color -
"lite"- lite shaded fill -
"custom"- will not update the fill, in case you manually adjusted these values
Border options:
-
"box"- will draw a border around each label **““- absence of”box”inlabel_style` will remove any border
The label_style string can be any string that contains those values, for example:
label_style="lite box"label_style="shaded"label_style="basic box"
vo3 <- venndir_label_style(vo,
inside_percent_threshold=0,
label_style="lite box")
render_venndir(vo3);
Text Venn for the R Console
There is a text Venn diagram, surprisingly useful for quickly checking overlaps and direction. Note that the R console, and R help examples display colored text, just not in Rmarkdown.
The first example is the basic Venn overlap, without direction.
setlist <- make_venn_test(1000, 3, do_signed=TRUE)
textvenn(setlist, overlap_type="overlap")
#> set_A&set_B
#> 27
#> set_A set_B
#> 31 390
#>
#> set_A&set_B&set_C
#> 7
#> set_A&set_C set_B&set_C
#> 6 76
#>
#>
#> set_C
#> 71But of course direction is helpful, so here it is with the default overlap_type="concordance" (below)
textvenn(setlist, overlap_type="concordance")
#> set_A&set_B ↑↑: 9
#> 27 ↓↓: 12
#> set_A ↑: 19 X: 6 set_B ↑: 185
#> 31 ↓: 12 390 ↓: 205
#>
#> set_A&set_B&set_C ↑↑↑: 2
#> 7 X: 5
#> set_A&set_C ↑↑: 2 set_B&set_C ↑↑: 39
#> 6 ↓↓: 3 76 ↓↓: 21
#> X: 1 X: 16
#>
#> set_C ↑: 30
#> 71 ↓: 41Not all consoles can display Unicode arrows, so you can use ASCII output only with unicode=FALSE:
textvenn(setlist, overlap_type="concordance", unicode=FALSE)
#> set_A&set_B ^^: 9
#> 27 vv: 12
#> set_A ^: 19 X: 6 set_B ^: 185
#> 31 v: 12 390 v: 205
#>
#> set_A&set_B&set_C ^^^: 2
#> 7 X: 5
#> set_A&set_C ^^: 2 set_B&set_C ^^: 39
#> 6 vv: 3 76 vv: 21
#> X: 1 X: 16
#>
#> set_C ^: 30
#> 71 v: 41Sorry, no proportional text Venn diagrams (yet)!
Nudge Venn circles
Another driving reason for this package is that sometimes proportional Venn (Euler) diagrams fail to produce circles that show all the overlaps. While sometimes it is mathematically impossible, other times are just… puzzling.
See below, the overlap set_A&set_B has 1 count, but is not displayed.
overlaps <- c(set_A=187, set_B=146, set_C=499,
`set_A&set_B`=1,
`set_A&set_C`=181,
`set_B&set_C`=219,
`set_A&set_B&set_C`=20);
# convert to setlist
setlist_o <- counts2setlist(overlaps)
venndir(setlist_o,
proportional=TRUE,
font_cex=1.4,
set_colors=c("firebrick2", "dodgerblue", "#9999AA"))
The argument circle_nudge lets you nudge (move) a Venn circle given x,y coordinates. Provide a list named by the set you want to move, with a numeric vector for the x,y coordinates direction.
vo_nudge <- venndir(setlist_o,
font_cex=1.4,
proportional=TRUE,
circle_nudge=list(set_A=c(1, 0), set_B=c(-1, 0)),
set_colors=c("firebrick2", "dodgerblue", "#9999AA"))
Item labels
An optional but useful feature is to include item labels inside the Venn diagram. It helps answer the question, “What are those shared items?” (In my experience, that’s a very early question.)
This step can also include the directional sign, which helps indicate which items are shared, and whether they have the same direction. In cases with too many labels to display, it is sometimes still useful to display the sign, as a visual cue for the proportion of shared or discordant signs.
Two arguments are required: the label_preset to define the visibility of items and main set labels; and show_items to define the type of item label. For example label_preset="main items" will display main set labels outside, and item labels inside; and show_items="item" will display the item label, show_items="sign item" will display the sign and item label, show_items="sign" will display only the sign.
setlist <- make_venn_test(100, 3, do_signed=TRUE);
venndir(setlist,
poly_alpha=0.3,
label_preset="main items",
show_items="sign item");
Interestingly, the density of labels gives some indication of the relative overlaps.
The same plot using proportional circles makes the label density effectively uniform:
setlist <- make_venn_test(100, 3, do_signed=TRUE);
venndir(setlist,
poly_alpha=0.3,
label_preset="main items",
show_items="item",
proportional=TRUE);
With too many features to label, it’s still interesting to indicate the sign.
setlist <- make_venn_test(1000, 3, do_signed=TRUE);
venndir(setlist,
label_preset="main items",
show_items="sign",
item_cex=3,
show_segments=FALSE,
max_items=10000);
Again, proportional Venn circles effectively makes the density uniform.
venndir(setlist,
label_preset="main items",
overlap_type="each",
show_items="sign",
item_cex=4,
max_items=10000,
show_segments=FALSE,
proportional=TRUE);