chargeHydropathyPlot {idpr} | R Documentation

## Charge-Hydropathy Plot

### Description

This function calculates the average net charge <R> and the average scaled hydropathy <H> and visualizes the data. There are known boundaries on the C-H plot that separate extended and collapsed proteins.
This was originally described in Uversky et al. (2000)
https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7 .
The plot returned is based on the charge-hydropathy plot from Uversky (2016) https://doi.org/10.1080/21690707.2015.1135015.
See Uversky (2019) https://doi.org/10.3389/fphy.2019.00010 for additional information and a recent review on the topic. This plot has also been referred to as a "Uversky Plot".

### Usage

    chargeHydropathyPlot(
      sequence,
      displayInsolubility = TRUE,
      insolubleValue = 0.7,
      proteinName = NA,
      customPlotTitle = NA,
      pH = 7,
      pKaSet = "IPC_protein",
      plotResults = TRUE,
      ...
    )

### Arguments

`sequence` | amino acid sequence (or pathway to a fasta file) as a character string. Supports multiple sequences / files, as a character vector of strings. Additionally, this supports a single protein as character vectors. Multiple proteins are not supported as a character vector of single characters.
`displayInsolubility` | logical value, TRUE by default. This adds (or removes when FALSE) the vertical line separating collapsed proteins and insoluble proteins
`insolubleValue` | numerical value. 0.7 by default. Ignored when `displayInsolubility = FALSE`. Plots the vertical line <H> = displayInsolubility.
`proteinName, customPlotTitle` | optional character string. NA by default. Used to either add the name of the protein to the plot title when there is only one protein, or to create a custom plot title for the output.
`pH` | numeric value, 7.0 by default. The environmental pH is used to calculate residue charge.
`pKaSet` | pKa set used for charge calculations. See `netCharge` for additional details
`plotResults` | logical value, TRUE by default. This determines what is returned. If `plotResults = FALSE`, a data frame is returned with the Sequence(s), Average Scaled Hydropathy, and Average Net Charge. If `plotResults = TRUE`, a graphical output is returned (ggplot) showing the Charge Hydropathy Plot (recommended).
`...` | additional arguments to be passed to idpr::netCharge(), idpr::meanScaledHydropathy() or `ggplot`

### Value

Graphical values of Charge-Hydropathy Plot

### Plot Colors

For users who wish to keep a common aesthetic, the following colors are used when plotResults = TRUE.

- Point(s) = "chocolate1" or "#ff7f24"

- Lines = "black"

### References

Kozlowski, L. P. (2016). IPC – Isoelectric Point Calculator. Biology Direct, 11(1), 55. https://doi.org/10.1186/s13062-016-0159-9
Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of molecular biology, 157(1), 105-132.
Uversky, V. N. (2019). Intrinsically Disordered Proteins and Their “Mysterious” (Meta)Physics. Frontiers in Physics, 7(10). https://doi.org/10.3389/fphy.2019.00010
Uversky, V. N. (2016). Paradoxes and wonders of intrinsic disorder: Complexity of simplicity. Intrinsically Disordered Proteins, 4(1), e1135015. https://doi.org/10.1080/21690707.2015.1135015
Uversky, V. N., Gillespie, J. R., & Fink, A. L. (2000). Why are “natively unfolded” proteins unstructured under physiologic conditions?. Proteins: structure, function, and bioinformatics, 41(3), 415-427. https://doi.org/10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7

### See Also

`netCharge` and `meanScaledHydropathy` for functions used to calculate values.

### 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
    chargeHydropathyPlot(sequence = aaString)
    chargeHydropathyPlot( sequence = aaVector)

    #This function also supports multiple sequences
    #only as character strings or .fasta files
    multipleSeq <- c("ACDEFGHIKLMNPQRSTVWY",
                   "ACDEFGHIK",
                   "LMNPQRSTVW")
    chargeHydropathyPlot(sequence = multipleSeq)

    #since it is a ggplot, we can add additional annotations or themes
    chargeHydropathyPlot(
     sequence = multipleSeq)  +
      ggplot2::theme_void()

    chargeHydropathyPlot(
      sequence = multipleSeq)  +
      ggplot2::geom_hline(yintercept = 0,
                         color = "red")

    #choosing the pKa set used for calculations
    chargeHydropathyPlot(
      sequence = multipleSeq,
      pKaSet = "EMBOSS")

[Package idpr version 1.0.007 Index]