getGroupingSymbol: Get character symbols for grouped amino acids

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

Get character symbols for grouped amino acids

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")

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