ssvFeatureVenn {seqsetvis}R Documentation

ggplot implementation of vennDiagram from limma package. currently limited at 3 sets. ssvFeatureUpset and ssvFeatureBinaryHeatmap are good options for more than 3 sets. ssvFeatureEuler can work too but can take a very long time to run for more than 5 or so.

Description

ggplot implementation of vennDiagram from limma package. currently limited at 3 sets. ssvFeatureUpset and ssvFeatureBinaryHeatmap are good options for more than 3 sets. ssvFeatureEuler can work too but can take a very long time to run for more than 5 or so.

Usage

ssvFeatureVenn(
  object,
  group_names = NULL,
  counts_txt_size = 5,
  counts_as_labels = FALSE,
  show_outside_count = FALSE,
  line_width = 3,
  circle_colors = NULL,
  fill_alpha = 0.3,
  line_alpha = 1,
  counts_color = NULL,
  n_points = 200,
  return_data = FALSE
)

Arguments

object

will be passed to ssvMakeMembTable for conversion to membership matrix

group_names

useful if names weren't provided or were lost in creating membership matrix

counts_txt_size

font size for count numbers

counts_as_labels

if TRUE, geom_label is used instead of geom_text. can be easier to read.

show_outside_count

if TRUE, items outside of all sets are counted outside. can be confusing.

line_width

uses size aesthetic to control line width of circles.

circle_colors

colors to use for circle line colors. Uses Dark2 set from RColorBrewer by default.

fill_alpha

alpha value to use for fill, defaults to .3.

line_alpha

numeric [0,1], alpha value for circle line

counts_color

character. single color to use for displaying counts

n_points

integer. number of points to approximate circle with. default is 200.

return_data

logical. If TRUE, return value is no longer ggplot and is instead the data used to generate that plot. Default is FALSE.

Value

ggplot venn diagram

Examples

ssvFeatureVenn(list(1:3, 2:6))
ssvFeatureVenn(CTCF_in_10a_overlaps_gr)
ssvFeatureVenn(S4Vectors::mcols(CTCF_in_10a_overlaps_gr)[,2:3])

[Package seqsetvis version 1.14.0 Index]