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

force.colour.scheme.Rd

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?

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).

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

Author

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');
#> [1] "darkseagreen4" "orchid4"       "slategrey"     "darkturquoise"
#> [5] "darkorange"    "darkorange4"   "gold1"         "slategrey"    
force.colour.scheme(annovar.output,'annovar.annotation', 'white');
#> [1] "darkseagreen4" "orchid4"       "white"         "darkturquoise"
#> [5] "darkorange"    "darkorange4"   "gold1"         "white"