How to edit ggVennDiagram intersection fill region

Question

I'm not using the global ggVennDiagram to edit individually each part of the plot.

I'm using a custom named vector to color the group variable, but I get a gray color for intersection region. I'm using alpha value, so I would like to have an overlap of my custom colors

Some idea? Thanks

library(ggVennDiagram)
library(ggplot2)

genes <- paste0("gene",1:40)

gene_list <- list(
  A = genes[1:10],
  B = genes[1:20],
  C = genes[5:15],
  D = genes[30:40]
)

venn <- Venn(gene_list)
d <- process_data(venn)

col <- c(A = 'blue', B = 'red', C = 'green', D = 'orange')

ggplot() +
  geom_sf(aes(fill = name), data = venn_region(d)) +
  geom_sf(aes(color = name), data = venn_setedge(d)) +
  geom_sf_text(aes(label = name), data = venn_setlabel(d)) +
  geom_sf_text(aes(label = count), data = venn_region(d)) +
  scale_fill_manual(values = alpha(col, .2)) +
  scale_color_manual(values = col) +
  theme_void()

gregor-fausto · Answer 1 · 2021-08-27T17:34:03.387

EDIT (original, incorrect answer below)

Here's another try at this. As far as I can tell this is a consequence of how the Venn diagram is being constructed. d@region is an object consisting of 15 polygons; ggplot is then looking for a color for each of them when we call geom_sf(aes(fill = name), data = venn_region(d)).

Here's an imperfect try at a solution. This duplicates the venn object (d2 <- process_data(venn)) and then creates polygons from the outlines of the shapes (d2@region <- st_polygonize(d@setEdge)). Those polygons are then used to plot the circles/fill.

library(ggVennDiagram)
library(ggplot2)
library(sf)

genes <- paste0("gene",1:40)

gene_list <- list(
A = genes[1:10],
B = genes[1:20],
C = genes[5:15],
D = genes[30:40]
)

venn <- Venn(gene_list)
d <- process_data(venn)
d2 <- process_data(venn)

d2@region <- st_polygonize(d@setEdge)

col <- c(A = 'blue', B = 'red', C = 'green', D = 'orange')

ggplot() +
geom_sf(aes(fill = name), data = venn_region(d2)) +
geom_sf(aes(color = name), data = venn_setedge(d)) +
geom_sf_text(aes(label = name), data = venn_setlabel(d)) +
geom_sf_text(aes(label = count), data = venn_region(d)) +
scale_color_manual(values = alpha(col, .2)) +
scale_fill_manual(values = alpha(col, .2)) +
theme_void()

I'm not getting a gray color for the intersection region, but instead a message that points to scale_fill_manual requiring more than 4 color values.

Following the answer to this StackOverflow post on creating a color gradient, it's possible to set a color gradient for the colors you provided. Those then get used to fill the regions of intersection, and the 4 colors are the outlines of the regions.

library(ggVennDiagram)
library(ggplot2)

genes <- paste0("gene",1:40)

gene_list <- list(
  A = genes[1:10],
  B = genes[1:20],
  C = genes[5:15],
  D = genes[30:40]
)
      
venn <- Venn(gene_list)
d <- process_data(venn)
    
# vector for colors
    colorGroups <- c(A = 'blue', B = 'red', C = 'green', D = 'orange')        
# use colorRampPalette to create function that interpolates colors 
    colfunc <- colorRampPalette(colorGroups)
# call function and create vector of 15 colors
    col <- colfunc(15)
    
ggplot() +
  geom_sf(aes(fill = name), data = venn_region(d)) +
  geom_sf(aes(color = name), data = venn_setedge(d)) +
  geom_sf_text(aes(label = name), data = venn_setlabel(d)) +
  geom_sf_text(aes(label = count), data = venn_region(d)) +
  scale_fill_manual(values = alpha(col, .2)) +
  scale_color_manual(values = colorGroups) +
  theme_void()

That's it, thanks a lot!!! I've run my code again, and I've not any message and get that gray color fill on intersection. I'm using cran version of ggVennDiagram v1.1.4. Your approach is correct and get the same plot — Archymedes, Aug 23 '21 at 09:06
Sorry, there is a problem with the composition of the palette. For example, the region A-C is not composed by blue-green, it has some of red — Archymedes, Aug 23 '21 at 17:04

How to edit ggVennDiagram intersection fill region

1 Answers1