plot_iRT {proBatch} | R Documentation

## Plot iRT measurements

### Description

Creates a iRT facetted ggplot2 plot of the value in `measure_col` vs `order_col` using `plot_single_feature`. Additionally, the resulting plot can also be facetted by batch.

### Usage

    plot_iRT(df_long, sample_annotation, peptide_annotation = NULL,
      protein_col = "ProteinName", order_col = "order",
      irt_pattern = "iRT", sample_id_col = "FullRunName",
      batch_col = "MS_batch", measure_col = "Intensity",
      feature_id_col = "peptide_group_label", color_by_batch = FALSE,
      color_scheme = "brewer", facet_by_batch = FALSE,
      color_by_col = NULL, color_by_value = NULL,
      plot_title = "iRT peptide profile", ...)

### Arguments

`df_long` | data frame where each row is a single feature in a single sample. It minimally has a `sample_id_col`, a `feature_id_col` and a `measure_col`, but usually also an `m_score` (in OpenSWATH output result file)
`sample_annotation` | data matrix with: `sample_id_col` (this can be repeated as row names) biological covariates technical covariates (batches etc)
`peptide_annotation` | long format data with peptide ID and their corresponding protein annotations
`protein_col` | column where protein names are specified
`order_col` | column in `sample_annotation` that determines sample order. It is used for certain diagnostics and normalisations.
`irt_pattern` | substring used to identify irts proteins in the column 'ProteinName'
`sample_id_col` | name of the column in sample_annotation file, where the filenames (colnames of the data matrix are found)
`batch_col` | column in `sample_annotation` that should be used for batch comparison
`measure_col` | if `df_long` is among the parameters, it is the column with expression/abundance/intensity; otherwise, it is used internally for consistency
`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.
`color_by_batch` | (logical) whether to color points by batch
`color_scheme` | color scheme for `ggplot` representation
`facet_by_batch` | (logical) whether to plot each batch in its own facet
`color_by_col` | column to color by certain value denoted by `color_by_value`
`color_by_value` | value in `color_by_col` to color
`plot_title` | the string indicating the source of the peptides
`...` | additional arguments to `plot_single_feature` function

### Value

ggplot2 type plot of `measure_col` vs `order_col`, faceted by `irt_pattern` containing proteins and (optionally) by `batch_col`

### See Also

Other feature-level diagnostic functions: `plot_peptides_of_one_protein`, `plot_single_feature`, `plot_spike_in`, `plot_with_fitting_curve`

### Examples

    irt_plot <- plot_iRT(example_proteome,
    example_sample_annotation,
    protein_col = 'Gene', irt_pattern = "BOVINE_A1ag")

[Package proBatch version 1.0.0 Index]