plot_peptide_corr_distribution {proBatch} | R Documentation

## Create violin plot of peptide correlation distribution

### Description

Plot distribution of peptide correlations within one protein and between proteins

### Usage

    plot_peptide_corr_distribution(
      data_matrix,
      peptide_annotation,
      protein_col = "ProteinName",
      feature_id_col = "peptide_group_label",
      filename = NULL,
      width = NA,
      height = NA,
      units = c("cm", "in", "mm"),
      plot_title = "Distribution of peptide correlation",
      theme = "classic"
    )

    plot_peptide_corr_distribution.corrDF(
      corr_distribution,
      filename = NULL,
      width = NA,
      height = NA,
      units = c("cm", "in", "mm"),
      plot_title = "Correlation of peptides",
      theme = "classic"
    )

### Arguments

`data_matrix` | features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. See "example_proteome_matrix" for more details (to call the description, use `help("example_proteome_matrix")`)
`peptide_annotation` | long format data frame with peptide ID and their corresponding protein and/or gene annotations. See `help("example_peptide_annotation")`.
`protein_col` | column where protein names are specified
`feature_id_col` | name of the column with feature/gene/peptide/protein ID used in the long format representation `df_long`. In the wide formatted representation `data_matrix` this corresponds to the row names.
`filename` | path where the results are saved. If null the object is returned to the active window; otherwise, the object is save into the file. Currently only pdf and png format is supported
`width` | option determining the output image width
`height` | option determining the output image width
`units` | units: 'cm', 'in' or 'mm'
`plot_title` | title of the plot (e.g., processing step + representation level (fragments, transitions, proteins) + purpose (meanplot/corrplot etc))
`theme` | ggplot theme, by default `classic`. Can be easily overriden
`corr_distribution` | data frame with peptide correlation distribution

### Value

`ggplot` object (violin plot of peptide correlation)

### See Also

`calculate_peptide_corr_distr`, `ggplot`

### Examples

    peptide_corr_distribution <- plot_peptide_corr_distribution(
    example_proteome_matrix,
    example_peptide_annotation, protein_col = 'Gene')

    selected_genes = c('BOVINE_A1ag','BOVINE_FetuinB','Cyfip1')
    gene_filter = example_peptide_annotation$Gene %in% selected_genes
    peptides_ann = example_peptide_annotation$peptide_group_label
    selected_peptides = peptides_ann[gene_filter]
    matrix_test = example_proteome_matrix[selected_peptides,]
    pep_annotation_sel = example_peptide_annotation[gene_filter, ]
    corr_distribution = calculate_peptide_corr_distr(matrix_test,
    pep_annotation_sel, protein_col = 'Gene')
    peptide_corr_distribution <- plot_peptide_corr_distribution.corrDF(corr_distribution)

    ## Not run:
    peptide_corr_distribution <- plot_peptide_corr_distribution.corrDF(corr_distribution,
    filename = 'test_peptide.png',
    width = 28, height = 28, units = 'cm')

    ## End(Not run)

[Package proBatch version 1.4.0 Index]