In jmw86069/venndir: Directional Venn diagrams

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venndir

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");

Why Venndir?

Biological data often involves components, for example genes, and the direction of change, for example increase or decrease. It is not enough to compare genes affected by two experiments, it is critical to compare the direction of change. How else can we discriminate the effects of disease from the effects of a cure?

# silence the warnings
options("warn"=-1)

library(venndir)
vo <- venndir(make_venn_test(100, 2, do_signed=TRUE),
   proportional=TRUE,
   overlap_type="each", font_cex=1.2)

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.

setlist <- make_venn_test(100, 3)
setlist

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. Add argument proportional=TRUE.

vo <- venndir(setlist,
   proportional=TRUE)

Venn Direction

The namesake of this package is Venn with directionality!

Test with: make_venn_test(..., do_signed=TRUE). Each item is associated with a numerical direction:

• +1 for up
• -1 for down

Each vector in setlist_dir is a named vector, whose names are the items, and whose values are the direction, with +1 or -1. Take a look.

setlist_dir <- make_venn_test(100, 3, do_signed=TRUE)
setlist_dir

For 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 is concordance=0.5. Concordance is a measure of how frequently two directions are the same, and is defined (agree - disagree) / (n). Thus, concordance=0 means there are the same number that agree as disagree in direction, and concordance=1 means 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"

This option 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 details.

Notice the "X" to indicate discordance.

venndir(setlist_dir)

overlap_type="each"

This option shows the count for each combination. It works best when you want to see all the details, however it can create a lot of labels!

venndir(setlist_dir, overlap_type="each")

overlap_type="agreement"

This option shows the count that agrees in direction, and the count that disagrees in direction. It does not indicate whether the agreement is up or down.

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"

This option only displays the overlap count, ignoring direction.

venndir(setlist_dir, overlap_type="overlap")

Proportional Venn Direction

As mentioned previously, you can display proportional Venn diagram, (a Euler diagram), which uses the excellent eulerr R package. Add argument proportional=TRUE.

vo <- venndir(setlist_dir,
   proportional=TRUE,
   font_cex=c(1.3, 0.9, 0.7))

Labeling is often a challenge with proportional Venn diagrams. For very small regions, you can push the label outside with inside_percent_threshold=5. This option will move labels outside when the region is less than 5% of the total area.

venndir(setlist,
   proportional=TRUE,
   overlap_type="overlap",
   label_style="lite box",
   inside_percent_threshold=5,
   font_cex=c(1.3, 1))

Customizing the Venn diagram

Label styles

The argument label_style can be used to customize the label:

• label_style="lite" - adds lite shading behind each label
• label_style="shaded" - adds partially transparent shading
• label_style="fill" - adds solid colored shading
• label_style="box" - adds a small outline box around the label

Multiple terms can be combined, for example to add shading and a box:

• label_style="shaded box" - adds colored shading and a box outline

Label position

Argument show_labels is used to position labels. Each letter defines a type of label, and UPPERCASE or lowercase indicates where to place the label.

• UPPERCASE = outside the Venn diagram
• lowercase = inside the Venn diagram

The letters:

• N = the set name
• C = the overlap count
• S = the signed overlap count(s)
• i = the overlapping items

Guidance:

• The default: show_labels="Ncs" will show _N_ame outside, _c_ounts inside. When _s_igned labels are shown, they also appear inside. Signed labels are not shown when overlap_type="overlap".
• Display all labels inside: show_labels="ncs"
• It works best to have the _c_ounts and _s_igned counts together, usually inside.
• To display items, show_labels="Ni" is recommended, to show _N_ame outside, and _i_tems inside. You can still use show_items="sign item" so that each item label will include the direction.
• When displaying items, the counts and signed counts are automatically moved outside. (There isn't a great way to place item labels around the count labels. Maybe in future.)

vo4 <- venndir(setlist,
   show_labels="ncs",
   inside_percent_threshold=0)

Hide line segments with show_segments=FALSE

vo4l <- venndir(setlist,
   show_labels="Ncs",
   show_segments=FALSE,
   inside_percent_threshold=0)

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.

# Options are used for the RMarkdown
# options("jam.htmlOut"=TRUE, "jam.comment"=FALSE)

setlist <- make_venn_test(1000, 3, do_signed=TRUE)
names(setlist) <- gsub("set_", "", names(setlist));
textvenn(setlist, overlap_type="overlap")

But of course direction is helpful, so here it is with the default overlap_type="concordance" (below)

textvenn(setlist, overlap_type="concordance")

Not all consoles can display Unicode arrows, so you can use ASCII output only with unicode=FALSE:

textvenn(setlist, overlap_type="concordance", unicode=FALSE)

# Revert options
# options("jam.htmlOut"=FALSE, "jam.comment"=TRUE)

Sorry, 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)

vn <- venndir(setlist_o,
   expand_fraction=0.15,
   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,
   expand_fraction=0.15,
   # label_style="lite box",
   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 changes are required:

1. Argument show_labels must include "i" to indicate items should be included in the labels. Preferred options:

2. "Ni" which shows _N_ame outside, and _i_tems inside.

3. "NCi" which shows _N_ame and _C_ounts outside, and _i_tems inside.

4. Argument show_items should be one of

5. "item" - to show only the item label

6. "sign item" - to show the sign beside each item label
7. "sign" - to show only the item label

setlist <- make_venn_test(100, 3, do_signed=TRUE);
venndir(setlist,
   poly_alpha=0.3,
   show_labels="NCi",
   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. Note the option show_items="sign" displays only the directional arrow, and item_cex=2 makes the arrows twice as large as normal.

setlist <- make_venn_test(100, 3, do_signed=TRUE);
venndir(setlist,
   poly_alpha=0.3,
   show_labels="Ni",
   item_cex=2,
   show_items="sign",
   proportional=TRUE);

The sign is an interesting visual summary when there are too many labels to display otherwise.

setlist <- make_venn_test(1000, 3, do_signed=TRUE);
venndir(setlist,
   show_labels="Ni",
   show_items="sign",
   item_cex=2,
   expand_fraction=0.1,
   show_segments=FALSE,
   max_items=10000);

Again, proportional Venn circles effectively makes the density uniform.

venndir(setlist,
   show_labels="Ni",
   overlap_type="each",
   show_items="sign",
   item_cex=2,
   expand_fraction=0.1,
   max_items=10000,
   show_segments=FALSE,
   proportional=TRUE)

jmw86069/venndir documentation built on Nov. 14, 2024, 10:12 a.m.