ssvFeatureVenn: ssvFeatureVenn

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

ssvFeatureVenn

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,
  counts_as_percent = FALSE,
  percentage_digits = 1,
  percentage_suffix = "%",
  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 value from 0 to 1. Alpha value for circle line
counts_color	character. single color to use for displaying counts
counts_as_percent	if TRUE, convert counts to percentages in plots.
percentage_digits	The number of digits to round percentages to, default is 1.
percentage_suffix	The character to append to percentages, default is "%".
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

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

ssvFeatureVenn(list(1:3, 2:6),
  counts_as_percent = TRUE,
  percentage_digits = 2)

ssvFeatureVenn(list(1:3, 2:6),
  counts_as_percent = TRUE,
  percentage_digits = 0,
  percentage_suffix = " %",
  counts_txt_size = 12)

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.