colorsets {dagLogo} | R Documentation

## Color sets for visualization.

### Description

Create color encoding for visualization of a peptide sequence logo.

### Usage

    colorsets(colorScheme = ls(envir = cachedEnv))

### Arguments

`colorScheme` | A character vector of length 1, determining the color scheme based on amino acid classification methods. The available `colorScheme` are ""no","bulkiness_Zimmerman","hydrophobicity_KD", "hydrophobicity_HW", "isoelectric_point_Zimmerman", "contact_potential_Maiorov", "chemistry_property_Mahler", "consensus_similarity_SF", "volume_Bigelow", "structure_alignments_Mirny", "polarity_Grantham", "sequence_alignment_Dayhoff", "bulkiness_Zimmerman_group", "hydrophobicity_KD_group", "hydrophobicity_HW_group", "charge_group", "contact_potential_Maiorov_group", "chemistry_property_Mahler_group", "consensus_similarity_SF_group", "volume_Bigelow_group", "structure_alignments_Mirny_group", "polarity_Grantham_group", "sequence_alignment_Dayhoff_group", "custom" and "custom_group". If "custom" or "custom_group" are used, users must define a grouping scheme using a list containing sublist named as "color", and "symbol" using the function addScheme, with group set as "NULL" or a list with same names as those of `color` and `symbol`. No grouping was applied for the first 12 schemes. It is used to color AAs based on similarities or group amino acids into groups of similarities..

### Value

A named character vector of colors

### Author(s)

Jianhong Ou, Haibo Liu

### See Also

`addScheme`

### Examples

    colorsets("polarity_Grantham_group")

[Package dagLogo version 1.26.2 Index]