colorsets: Color sets for visualization.

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

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")

dagLogo documentation built on Dec. 5, 2020, 2 a.m.