getGroupingSymbol: Get character symbols for grouped amino acids

In haibol2016/dagLogo: dagLogo: a bioconductor package for visualizeing conserved amino acid sequence pattern in groups based on probability theory

Description

Get character symbols for grouped amino acids

Usage

getGroupingSymbol(groupingScheme = ls(envir = cachedEnv))

Arguments

groupingScheme

A character vector of length 1, determining the character symbols used to represent amino acids grouped by their physical and chemical properties. The available groupingScheme 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", and "custom". If "custom" is used, users must define a grouping scheme using a list containing sublists named as "color", "symbol" and "group" using the function addScheme. No grouping was applied for the first 12 schemes.

Value

A named character vector of character symbols if grouping is applied; otherwise NULL.

Author(s)

Jianhong Ou, Haibo Liu

See Also

addScheme

Examples

getGroupingSymbol("polarity_Grantham_group")

haibol2016/dagLogo documentation built on June 28, 2020, 1:31 a.m.