circos_plus_minus: Write tiles of bacterial ontology groups using the categories...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Write tiles of bacterial ontology groups using the categories from microbesonline.org.

Description

This function tries to save me from writing out ontology definitions and likely making mistakes. It uses the start/ends from the gff annotation along with the 1 letter GO-like categories from microbesonline.org. It then writes two data files circos/data/bob_plus_go.txt, circos/data/bob_minus_go.txt along with two configuration files circos/conf/bob_minus_go.conf and circos/conf/bob_plus_go.conf and finally adds an include to circos/bob.conf

Usage

circos_plus_minus(
  cfg,
  outer = 1,
  width = 0.08,
  thickness = 95,
  spacing = 0,
  padding = 1,
  margin = 0,
  plus_orientation = "out",
  minus_orientation = "in",
  layers = 1,
  layers_overflow = "hide",
  acol = "orange",
  bcol = "reds-9-seq",
  ccol = "yellow",
  dcol = "vlpurple",
  ecol = "vlgreen",
  fcol = "dpblue",
  gcol = "vlgreen",
  hcol = "vlpblue",
  icol = "vvdpgreen",
  jcol = "dpred",
  kcol = "orange",
  lcol = "vvlorange",
  mcol = "dpgreen",
  ncol = "vvlpblue",
  ocol = "vvlgreen",
  pcol = "vvdpred",
  qcol = "ylgn-3-seq",
  rcol = "vlgrey",
  scol = "grey",
  tcol = "vlpurple",
  ucol = "greens-3-seq",
  vcol = "vlred",
  wcol = "vvdppurple",
  xcol = "black",
  ycol = "lred",
  zcol = "vlpblue",
  max = NULL,
  label_column = NULL,
  url_string = ""
)

Arguments

cfg	Result from circos_prefix().
outer	Floating point radius of the circle into which to place the plus-strand data.
width	Radial width of each tile.
thickness	How wide to make the bars.
spacing	Radial distance between outer, inner, and inner to whatever follows.
padding	How much space between them.
margin	Margin between elements.
plus_orientation	Orientation of the plus pieces.
minus_orientation	Orientation of the minus pieces.
layers	How many layers to use
layers_overflow	How to handle too many layers.
acol	A color: RNA processing and modification. (orange)
bcol	B color: Chromatin structure and dynamics. (red-9)
ccol	C color: Energy production conversion. (yellow)
dcol	D color: Cell cycle control, mitosis and meiosis. (very light purple)
ecol	E color: Amino acid transport metabolism. (very light green)
fcol	F color: Nucleotide transport and metabolism. (deep blue)
gcol	G color: Carbohydrate transport and metabolism. (very light green)
hcol	H color: Coenzyme transport and metabolism. (very light purple blue)
icol	I color: Lipid transport and metabolism. (very very deep green)
jcol	J color: Translation, ribosome structure and biogenesis. (deep red)
kcol	K color: Transcription. (orange)
lcol	L color: Replication, recombination, and repair. (very very light orange)
mcol	M color: Cell wall/membrane biogenesis. (deep green)
ncol	N color: Cell motility (very very light purple blue)
ocol	O color: Posttranslational modification, protein turnover, chaperones. (very very light green)
pcol	P color: Inorganic ion transport and metabolism. (very very deep red)
qcol	Q color: Secondary metabolite biosynthesis, transport, and catabolism. (very light green 3)
rcol	R color: General function prediction only. (very light grey)
scol	S color: Function unknown. (grey)
tcol	T color: Signal transduction mechanisms. (very light purple)
ucol	U color: Intracellular trafficking(sp?) and secretion. (green 3)
vcol	V color: Defense mechanisms. (very light red)
wcol	W color: Extracellular structures. (very very deep purple)
xcol	X color: Not in COG. (black)
ycol	Y color: Nuclear structure. (light red)
zcol	Z color: Cytoskeleton. (very light purple blue)
max	Maximum length for chromosomal lengths
label_column	Use this column for labelling interactive svg outptus.
url_string	printf formatting string for interactive svg outputs.

Value

Radius after adding the plus/minus information and the spacing between them.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.