plot_protein_corrplot {proBatch} | R Documentation

## Peptide correlation matrix (heatmap)

### Description

Plots correlation plot of peptides from a single protein

### Usage

    plot_protein_corrplot(data_matrix, protein_name, peptide_annotation,
      protein_col = "ProteinName", feature_id_col = "peptide_group_label",
      flavor = c("pheatmap", "corrplot"), filename = NULL, width = NA,
      height = NA, unit = c("cm", "in", "mm"),
      plot_title = sprintf("Peptide correlation matrix of %s protein",
      protein_name), ...)

### Arguments

`data_matrix` | features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. Usually the log transformed version of the original data
`protein_name` | the name of the protein
`peptide_annotation` | df with peptides and their corresponding proteins
`protein_col` | the column name in `peptide_annotation` with protein names
`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.
`flavor` | either corrplot from 'corrplot' package or heatmap, as in 'pheatmap'
`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
`unit` | units: 'cm', 'in' or 'mm'
`plot_title` | The title of the plot
`...` | parameters for the corrplot visualisation

### Value

`corrplot` or `pheatmap` object depending on `flavor`

### Examples

    protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix, protein_name = 'Haao',
                   peptide_annotation = example_peptide_annotation,
                   protein_col = 'Gene', flavor = "pheatmap")

[Package proBatch version 1.0.0 Index]