Skip to contents

Find Venn polygon overlaps

Source: R/venndir-polyclip.R
find_venn_overlaps_JamPolygon.Rd

Find Venn polygon overlaps

Usage

find_venn_overlaps_JamPolygon(
  jp,
  venn_counts = NULL,
  venn_items = NULL,
  venn_colors = NULL,
  sep = "&",
  preset = "dichromat2",
  blend_preset = "ryb",
  do_plot = FALSE,
  verbose = FALSE,
  ...
)

Arguments

jp

JamPolygon that contains one polygon per set, named using set names.

venn_counts

vector with integer values, whose names represent each Venn overlap set combination, using sep as delimiter between set names.

venn_items

list or NULL that contains items in each overlap set.

sep

character string used as a delimiter between set names.

preset, blend_preset

character string passed to colorjam::rainbowJam() and colorjam::blend_colors(), respectively, to define the color hue wheel used for categorical colors, and for color blending. The default preset="dichromat2" chooses color-blindness-friendly categorical colors, and blend_preset="ryb" blends multiple colors using a red-yellow-blue color wheel, consistent with paint-type color combinations.

do_plot

logical indicating whether to plot the output SpatialPolygonsDataFrame object.

verbose

logical indicating whether to print verbose output.

...

additional arguments are passed to supporting functions colorjam::group2colors(), colorjam::blend_colors(), nudge_sp().

Value

JamPolygon object, which contains columns:

  • "name"

  • "x", "y"

  • "fill"

  • "venn_name"

  • "venn_count"

  • "venn_items"

  • "venn_color"

  • "label"

  • "label_x"

  • "label_y"

Details

This function takes a named list of polygons and returns the combination of polygon overlaps as used in a Venn diagram.

When a vector of Venn counts is supplied, the counts are associated with the respective polygon, and any counts not represented by a polygon are returned as an attribute "venn_missing".

See also

Other JamPolygon: JamPolygon-class, Venndir-class, [,JamPolygon,ANY,ANY,ANY-method, add_orientation_JamPolygon(), area_JamPolygon(), bbox_JamPolygon(), buffer_JamPolygon(), check_JamPolygon(), check_Venndir(), eulerr_to_JamPolygon(), farthest_point_JamPolygon(), has_point_in_JamPolygon(), intersect_JamPolygon(), label_fill_JamPolygon(), label_outside_JamPolygon(), label_segment_JamPolygon(), labelr_JamPolygon(), minus_JamPolygon(), nearest_point_JamPolygon(), nudge_JamPolygon(), plot.JamPolygon(), point_in_JamPolygon(), polyclip_to_JamPolygon(), polygon_circles(), polygon_ellipses(), sample_JamPolygon(), split_JamPolygon(), union_JamPolygon(), update_JamPolygon()

Examples

# simple Venn circles
test_counts <- c(A=5, B=10, C=3, `B&C`=2)
x <- eulerr::euler(test_counts)
jp1 <- eulerr_to_JamPolygon(x)
polygon_colors <- colorjam::rainbowJam(length(jp1))
jp1@polygons$fill <- polygon_colors;
plot(jp1)


xo <- find_venn_overlaps_JamPolygon(jp=jp1, venn_counts=test_counts)
xo@polygons$outerborder <- jamba::makeColorDarker(darkFactor=1.2,
   xo@polygons$venn_color)
xo@polygons$outerborder.lwd <- 4;
plot(xo);


testlist <- list(set_A=LETTERS, set_B=LETTERS[1:10], set_C=LETTERS[7:11])
so <- subset(signed_overlaps(testlist), count > 0)
test_counts <- setNames(so$count, so$sets)
x <- eulerr::euler(test_counts)
jp1 <- eulerr_to_JamPolygon(x)
jp1@polygons$fill <- polygon_colors;
plot(jp1)

xo <- find_venn_overlaps_JamPolygon(jp=jp1, venn_counts=test_counts, verbose=TRUE)
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): names(jp):set_A,set_B,set_C 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): head(el1): 
#>                   set_A set_B set_C
#> set_A                 1     0     0
#> set_B                 0     1     0
#> set_C                 0     0     1
#> set_A&set_B           1     1     0
#> set_A&set_C           1     0     1
#> set_B&set_C           0     1     1
#> set_A&set_B&set_C     1     1     1
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): set_A 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichYes:1 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichNo:2,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): intersect_JamPolygon(jp[whichYes, ]), whichYes: 1 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): minus_JamPolygon(jp[whichNo, ]), whichNo: 2,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): length(overlap polygon):2 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): set_B 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichYes:2 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichNo:1,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): intersect_JamPolygon(jp[whichYes, ]), whichYes: 2 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): minus_JamPolygon(jp[whichNo, ]), whichNo: 1,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): length(overlap polygon):0 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): set_C 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichYes:3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichNo:1,2 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): intersect_JamPolygon(jp[whichYes, ]), whichYes: 3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): minus_JamPolygon(jp[whichNo, ]), whichNo: 1,2 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): length(overlap polygon):0 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): set_A&set_B 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichYes:1,2 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichNo:3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): intersect_JamPolygon(jp[whichYes, ]), whichYes: 1,2 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): minus_JamPolygon(jp[whichNo, ]), whichNo: 3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): length(overlap polygon):1 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): set_A&set_C 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichYes:1,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichNo:2 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): intersect_JamPolygon(jp[whichYes, ]), whichYes: 1,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): minus_JamPolygon(jp[whichNo, ]), whichNo: 2 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): length(overlap polygon):1 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): set_B&set_C 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichYes:2,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichNo:1 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): intersect_JamPolygon(jp[whichYes, ]), whichYes: 2,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): minus_JamPolygon(jp[whichNo, ]), whichNo: 1 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): length(overlap polygon):0 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): set_A&set_B&set_C 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichYes:1,2,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): whichNo: 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): intersect_JamPolygon(jp[whichYes, ]), whichYes: 1,2,3 
#> ##  (20:59:34) 09Dec2024:   find_venn_overlaps_JamPolygon(): length(overlap polygon):1 
#> ##  (20:59:34) 09Dec2024:   find_vennpoly_overlaps(): vennUse:1,4,5,7, vennMissing:2,3,6 
xo@polygons$outerborder <- jamba::makeColorDarker(darkFactor=1.2,
   xo@polygons$venn_color)
xo@polygons$outerborder.lwd <- 4;
plot(xo);