force.colour.scheme: Based on predefined colour schemes, returns a vector of...

In BoutrosLab.plotting.general: Functions to Create Publication-Quality Plots

Based on predefined colour schemes, returns a vector of corresponding colours.

Description

Takes a vector of character strings and an scheme returns the matching colours as a vector.

Usage

force.colour.scheme(
	x = NA,
	scheme,
	fill.colour = 'slategrey',
	include.names = FALSE,
	return.factor = FALSE,
	return.scheme = FALSE
	);

Arguments

x	The input character or numeric vector, defaults to NA incase return.scheme = TRUE.
scheme	A string representing a predefined scheme. Available schemes are: “annovar.annotation”, “annovar.annotation.collapsed”, “annovar.annotation.collapsed2”, “tissue”, “sex”, “stage”, “risk”, “MSI”, “tumour”, “CNV”, “organism”

, “chromosome” and “biomolecule”

fill.colour	Value to enter when value of x not present in scheme.
include.names	Should the output be a named vector or not?
return.factor	Should factors (scheme names) be returned?
return.scheme	Should the scheme list be returned?

Details

The input character options for each colour scheme are as follows: annovar.annotation

• nonsynonymous snv

• stopgain snv

• stoploss snv

• frameshift deletion

• frameshift substitution

• splicing

• synonymous snv

annovar.annotation.collapsed

• nonsynonymous snv

• stopgain snv

• stoploss SNV

• frameshift indel

• splicing

annovar.annotation.collapsed2

• nonsynonymous

• stopgain-stoploss

• splicing

• frameshift indel

• synonymous

• utr5-utr3

• nonframeshift indel

• intronic

• intergenic

• other

tissue

• cartilage

• bone

• adipose

• bladder

• kidney

• blood

• heart

• muscle

• hypothalamus

• pituitary

• thyroid

• parathyroid

• skin

• salivarygland

• esophagus

• stomach

• liver

• gallbladder

• pancreas

• intestine

• colon

• pharynx

• larynx

• trachea

• diaphragm

• lung

• nerve

• spine

• brain

• eye

• breast

• ovary

• uterus

• prostate

• testes

• lymph

• leukocyte

• spleen

sex

• male

• female

stage

• I

• II

• III

• IV

risk

• High

• Low

MSI

• MSI-High

• MSI-Low

• MSS

tumour

• Primary

• Metastatic

CNV

• Amplification

• Deletion

• LOH

• Neutral

organism

• Human

• Rat

• Mouse

chromosome

• 1 - 22

• X

• Y

biomolecule

• DNA

• RNA

• Protein

• Carbohydrate

• Lipid

clinicalt3

• t0

• t1

• t2

• t3

• t4

• t5

clinicalt9

• t1a

• t1b

• t1c

• t2a

• t2b

• t2c

• t3a

• t3b

• t3c

gleason.score

• 3+3

• 3+4

• 4+4

• 4+5

• 3+5

• 5+3

• 5+4

• 5+5

• missing

• NA

gleason.sum

• 5

• 6

• 7

• 8

• 9

• missing

• NA

tissue.color

• blood

• frozen

• ffpe

psa.categorical

• 0 - 9.9

• 10 - 19.9

• >= 20

age.categorical.default

• <50

• 50 - 60

• 60 - 70

• >= 70

age.categorical.prostate

• <40

• 40 - 50

• 50 - 65

• 65 - 70

• >= 70

age.gradient

psa.gradient

heteroplasmy

• 0 - 0.2

• 0.2 - 0.4

• 0.4 - 0.6

• 0.6 - 1.0

mt.annotation

• MT-DLOOP

• MT-T*

• MT-RNR*

• MT-ND1

• MT-ND2

• MT-ND3

• MT-ND4L

• MT-ND4L/MT-ND4

• MT-ND4

• MT-ND5

• MT-ND6

• MT-CO1

• MT-CO2

• MT-CO3

• MT-ATP6/MT-CO3

• MT-ATP6

• MT-ATP8/MT-ATP6

• MT-ATP8

• MT-CYB

• MT-NC*

• MT-OL*

isup.grade

• 1

• 2

• 3

• 4

• 5

Value

If multiple returns are requested, outputs a list (return.factor: factor length x with scheme names; scheme: list containing scheme names and colours; colours: vector length x with the required colours).

Author(s)

Nicholas Harding

Examples

annovar.output <- c('nonsynonymous snv', 'stopgain snv', 'none', 'stoploss snv', 
'frameshift deletion', 'frameshift substitution', 'splicing', 'none');
force.colour.scheme(annovar.output,'annovar.annotation');
force.colour.scheme(annovar.output,'annovar.annotation', 'white');

BoutrosLab.plotting.general documentation built on Nov. 2, 2023, 6:01 p.m.