sequenceMapCoordinates {idpr} | R Documentation

## Sequence Map Coordinates

### Description

This is a function used to create a coordinate grid for the `sequenceMap` function. It is based on the length of the sequence being mapped, and how many residues per line are specified. The function wraps the sequence to have a number of columns that is the sequence length / number of residues per row, rounded up.
This is intended for use within the sequenceMap function, however, this can also be used to identify the coordinates of residues within the ggplot coordinate plane for addition annotations.

### Usage

    sequenceMapCoordinates(sequence, nbResidues = 30)

### Arguments

`sequence` | amino acid sequence as a single character string, a vector of single characters, or an AAString object. It also supports a single character string that specifies the path to a .fasta or .fa file.
`nbResidues` | numeric value, 30 by default. The number of residues to display on each row of the plot. It is not recommended to be over 50 or under 10 for standard sequences. Optimal value may vary between sequences of extreme lengths.

### Value

A data frame with rows containing the amino acid sequence, residue position within the sequence, as well as the row and column of each residue within the ggplot output of sequenceMap().

### See Also

`sequenceMapCoordinates` for mapping coordinates

### Examples

    #Amino acid sequences can be character strings
    aaString <- "ACDEFGHIKLMNPQRSTVWY"
    #Amino acid sequences can also be character vectors
    aaVector <- c("A", "C", "D", "E", "F",
               "G", "H", "I", "K", "L",
               "M", "N", "P", "Q", "R",
               "S", "T", "V", "W", "Y")
    #Alternatively, .fasta files can also be used by providing
    ##The path to the file as a character string

    exampleDF <- sequenceMapCoordinates(aaString,
                                      nbResidues = 10)
    head(exampleDF)

    exampleDF <- sequenceMapCoordinates(aaVector,
                                     nbResidues = 10)
    head(exampleDF)

    #Getting a data frame for plotting with sequenceMap
     tendencyDF <- structuralTendency(sequence = aaVector)
     #Making a sequenceMap ggplot to annotate
    gg <- sequenceMap(sequence = tendencyDF$AA,
                property = tendencyDF$Tendency,
                 nbResidues = 3,
                  labelType = "both")

    #Change the nbResidues to correspond to the sequenceMap setting
    mapCoordDF <- sequenceMapCoordinates(aaVector,
                                      nbResidues = 3)
    head(mapCoordDF)

    #subsetting for positive residues
    mapCoordDF_subset <- mapCoordDF$AA %in% c("K", "R", "H")
    mapCoordDF_subset <- mapCoordDF[mapCoordDF_subset,]

    #use mapCoordDF to annotate positive residues with a plus
    library(ggplot2)
    gg <- gg + geom_point(inherit.aes = FALSE,
                        data = mapCoordDF_subset,
                       aes(x = col + 0.5, #to center on the residue
                           y = row + 0.2), #to move above on the residue
                       color = "purple",
                       size = 3,
                       shape = 3)
    plot(gg)

[Package idpr version 1.0.007 Index]