showGeneContent: Draw a bubble plot and two bar plots to summarise gene and...

In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes

Draw a bubble plot and two bar plots to summarise gene and allele frequencies.

Description

Use the function countAlleles and calcGeneFreq to know allele and gene content before using this function, in order to set appropriate graphic arguments. The diameter of each bubble is porportional to the allele number.

Dependency: ggplot2.

Usage

showGeneContent(
  af,
  gf,
  pam.g,
  d.min = 2,
  d.max = 20,
  fill.colour,
  border.colour = "grey90",
  core.genes = NULL,
  bar.acc = FALSE,
  panel.names = c("a", "b", "c"),
  panelA.xmax = 120,
  panelB.xinterv = 5,
  panelB.yinterv = 20,
  panelB.col = "grey50",
  panelC.lwd = 1,
  panelC.xinterv = 20,
  prev.out = NULL,
  f = "gene_content.png",
  w = 170,
  h = 200,
  r = 300,
  u = "mm",
  img.oma = c(0.1, 0.1, 0.1, 0.1),
  img.mar = c(3, 2.6, 1, 0.5),
  img.mgp = c(1.8, 0.6, -0.2)
)

Arguments

af	A table of allele frequencies, produced by the function countAlleles.
gf	A table of gene frequencies, produced by the function calcGeneFreq.
d.min	Diameter for genes of the minimum allele count.
d.max	Diameter for genes of the largest allele count.
fill.colour	A named vector of colours filling bubbles.
border.colour	A single colour for borders of circles.
core.genes	Names of core genes
bar.acc	Whether to draw a bar plot of gene frequencies for accessory genes (TRUE) or all genes (FALSE, default).
panel.names	A character vector of three elements for panel names. Default: a, b, c.
panelA.xmax	Maximum on the X axis of panel a for gene frequencies. Default: 120.
panelB.xinterv	Distance between major ticks on the X axis of the first bar plot (panel b). Default: 5.
panelB.yinterv	Distance between major ticks on the Y axis of the first bar plot (panel b). Default: 20.
panelB.col	Colour for a bar plot in the panel b. Default: grey50.
panelC.lwd	An integer specifying the width of bars for allele frequencies in the panel c. Default: 1.
panelC.xinterv	Distance between major ticks on the X axis of the second bar plot (panel b). Default: 50.
prev.out	Output from a previous run of this function.
f	Name for the output PNG file. Default: gene_content.png.
w	Image width.
h	Image height.
r	Image resolution.
u	Unit for the image width and height.
img.oma	The argument oma for the function par during plotting.
img.mar	The argument mar for the function par.
img.mgp	The argument mgp for the function par.

Author(s)

Yu Wan ([e-mail])

wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.