flower_plot: Flower plot could be treated as one kind of venn diagram but...

In Tong-Chen/YSX: For Yishengxin Training

Description

Flower plot could be treated as one kind of venn diagram but only showing common items like OTUs or genes among all groups and total items (or total items excluding common items) for each group.

Usage

flower_plot(
  input,
  sep = "\t",
  row.names = NULL,
  header = T,
  quote = "",
  comment = "",
  check.names = F,
  item_variable = NULL,
  set_variable = NULL,
  start = 90,
  a = 0.5,
  b = 2,
  r = 1,
  group_color = "Spectral",
  group_color_alpha = 0.6,
  label_total_num_items = TRUE,
  saveplot = NULL,
  label = "core",
  common_color = "white",
  common_color_alpha = 1,
  saveppt = FALSE,
  ...
)

Arguments

input	Input data file (first line as header line, the first column is the name of genes or OTUs or otehr things one wants to compare, the second column is the group name which genes belong to, tab seperated) Gene Sample g1 Set1 a1 Set3 b4 Set1 . . c1 Set3
start	Start position of first ellipse. Default 90 represents starting from 0 clock.
a	Vectors, radii of the ellypses along the two axes in user units.
b	Vectors, radii of the ellypses along the two axes in user units.
r	Set the size of the center circle.
group_color	Set the color of the petal ellipse (each group), with input format，like：c('#6181BD4E','#F348004E','#64A10E4E'...) or supply a RColorBrewer color set like "Set1", "Set2", "Set3", "YlOrRd" (check http://www.sthda.com/english/wiki/colors-in-r for more).
group_color_alpha	The transparency of each ellipse color. Default 0.6.
label_total_num_items	Label total number of items in for each group (when True) or label number of items in each group after substracting numbe of common items.
saveplot	Save plot to given file "a.pdf", "b.png".
label	The name of the center circle.
common_color	The color of the center circle. Default "white".
...	Parameters givento base_plot_save
common_col_alpha	The transparency of common circle color. Default 0.6.

Value

An image

Examples

flowerinput <- "test.file"
flower(flowerinput)

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.