addScheme: Add a custom coloring or grouping scheme.

In jianhong/dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

Add a custom coloring or grouping scheme.

Description

Add a custom coloring or grouping scheme for ungrouped or grouped amino acids as desired.

Usage

addScheme(
  color = vector("character"),
  symbol = vector("character"),
  group = NULL
)

Arguments

color	A named vector of character. This vector specifies different colors for visualizing the different amino acids or amino acid groups.
symbol	A named vector of character. This vector specifies the different symbols for visualizing the different amino acids or amino acid groups.
group	A list or NULL. If only coloring amino acids of similar property is desired, set group to NULL; otherwise group should be a list with same names as those of color and symbol.

Value

Add the custom coloring or grouping scheme to the environment cacheEnv.

Examples

## Add a grouping scheme based on the BLOSUM50 level 3 
color = c(LVIMC = "#33FF00", AGSTP = "#CCFF00",
         FYW = '#00FF66', EDNQKRH = "#FF0066")
symbol = c(LVIMC = "L", AGSTP = "A", FYW = "F", EDNQKRH = "E")
group = list(
   LVIMC = c("L", "V", "I", "M", "C"), 
   AGSTP = c("A", "G", "S", "T", "P"),
   FYW = c("F", "Y", "W"),
   EDNQKRH = c("E", "D", "N", "Q", "K", "R", "H"))
addScheme(color = color, symbol = symbol, group = group) 

jianhong/dagLogo documentation built on Nov. 5, 2024, 7:46 a.m.