vennplot: Draw an area-proportional Venn diagram of 2 or 3 circles...
In wangjiaxuan666/xbox: author's packages for himself

vennplot

R Documentation

Draw an area-proportional Venn diagram of 2 or 3 circles change by wangjiaxuan

Description

The function from bioVenn R packages(https://cran.r-project.org/web/packages/BioVenn/index.html), I improve the data output and delete the 'output' parameter. on the next step , I want be add the ggplot2 on the function which draw venn plot. or change the postion of group title name whcih is on the circ point now.

Usage

vennplot(
  list_x = NULL,
  list_y = NULL,
  list_z = NULL,
  title = "Venn Plot",
  subtitle = "Creat diagram by R packages xbox",
  t_f = "serif",
  t_fb = 2,
  t_s = 1.5,
  t_c = "black",
  st_f = "serif",
  st_fb = 4,
  st_s = 1.5,
  st_c = "black",
  xtitle = "X Set",
  xt_f = "serif",
  xt_fb = 2,
  xt_s = 1.5,
  xt_c = "white",
  ytitle = "Y Set",
  yt_f = "serif",
  yt_fb = 2,
  yt_s = 1.5,
  yt_c = "white",
  ztitle = "Z Set",
  zt_f = "serif",
  zt_fb = 2,
  zt_s = 1.5,
  zt_c = "white",
  nrtype = "abs",
  nr_f = "serif",
  nr_fb = 2,
  nr_s = 1,
  nr_c = "black",
  x_c = "#02786A",
  y_c = "#D23918",
  z_c = "#4C8045",
  bg_c = "white",
  width = 100,
  height = 100,
  filename = NULL
)

Arguments

`list_x`	(Required) List with IDs from dataset X
`list_y`	(Required) List with IDs from dataset Y
`list_z`	(Required) List with IDs from dataset Z
`title`	(Optional) The title of the Venn diagram
`subtitle`	(Optional) The subtitle of the Venn diagram (default is "(C) 2007-2020 Tim Hulsen")
`t_f`	(Optional) The font of the main title (default is "serif")
`t_fb`	(Optional) The font "face" of the main title (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)
`t_s`	(Optional) The size of the main title (cex; relative to the standard size; default is 1.5)
`t_c`	(Optional) The colour of the main title (default is "black")
`st_f`	(Optional) The font of the subtitle (default is "serif")
`st_fb`	(Optional) The font "face" of the subtitle (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)
`st_s`	(Optional) The size of the subtitle (cex; relative to the standard size; default is 1.2)
`st_c`	(Optional) The colour of the subtitle (default is "black")
`xtitle`	(Optional) The X title of the Venn diagram (default is "ID set X")
`xt_f`	(Optional) The font of the X title (default is "serif")
`xt_fb`	(Optional) The font "face" of the X title (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)
`xt_s`	(Optional) The size of the X title (cex; relative to the standard size; default is 1)
`xt_c`	(Optional) The colour of the X title (default is "black")
`ytitle`	(Optional) The Y title of the Venn diagram (default is "ID set Y")
`yt_f`	(Optional) The font of the Y title (default is "serif")
`yt_fb`	(Optional) The font "face" of the Y title (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)
`yt_s`	(Optional) The size of the Y title (cex; relative to the standard size; default is 1)
`yt_c`	(Optional) The colour of the Y title (default is "black")
`ztitle`	(Optional) The Z title of the Venn diagram (default is "ID set Z")
`zt_f`	(Optional) The font of the Z title (default is "serif")
`zt_fb`	(Optional) The font "face" of the Z title (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)
`zt_s`	(Optional) The size of the Z title (cex; relative to the standard size; default is 1)
`zt_c`	(Optional) The colour of the Z title (default is "black")
`nrtype`	(Optional) The type of the numbers to be displayed: absolute (abs) numbers or percentages (pct) (default is "abs")
`nr_f`	(Optional) The font of the numbers (default is "serif")
`nr_fb`	(Optional) The font "face" of the numbers (1=plain, 2=bold, 3=italic, 4=bold-italic; default is 2)
`nr_s`	(Optional) The size of the numbers (cex; relative to the standard size; default is 1)
`nr_c`	(Optional) The colour of the numbers (default is "black")
`x_c`	(Optional) The colour of the X circle (default is "red")
`y_c`	(Optional) The colour of the X circle (default is "green")
`z_c`	(Optional) The colour of the X circle (default is "blue")
`bg_c`	(Optional) The background colour (default is "white")
`width`	(Optional) The width of the output file (in pixels for BMP/JPEG/PNG/TIF or in centiinch for PDF/SVG; default is 1000)
`height`	(Optional) The height of the output file (in pixels for BMP/JPEG/PNG/TIF or in centiinch for PDF/SVG; default is 1000)
`filename`	(Optional) The name of the output file (default is "biovenn" + extension of the selected output format)

Details

This function creates an area-proportional Venn diagram of 2 or 3 circles, based on lists of (biological) identifiers. It requires three parameters: input lists X, Y and Z. For a 2-circle Venn diagram, one of these lists should be left empty. Duplicate identifiers are removed automatically, and a mapping from Entrez and/or Affymetrix to Ensembl IDs is available. BioVenn is case-sensitive. In SVG mode, text and numbers can be dragged and dropped.

When using a BioVenn diagram for a publication, please cite: BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams T. Hulsen, J. de Vlieg and W. Alkema, BMC Genomics 2008, 9 (1): 488

Value

An image of the Venn diagram is generated in the desired output format.

Also returns an object with thirteen lists: X, Y, Z, X only, Y only, Z only, XY, XZ, YZ, XY only, XZ only, YZ only, XYZ.

Examples

list_x <- c("1007_s_at","1053_at","117_at","121_at","1255_g_at","1294_at")
list_y <- c("1255_g_at","1294_at","1316_at","1320_at","1405_i_at")
list_z <- c("1007_s_at","1405_i_at","1255_g_at","1431_at","1438_at","1487_at","1494_f_at")
biovenn <- vennplot(list_x, list_y, list_z, subtitle="Example diagram", nrtype="abs")

wangjiaxuan666/xbox documentation built on Sept. 4, 2024, 5:03 p.m.