plot_single_feature {proBatch} | R Documentation

## Plot peptide measurements

### Description

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

### Usage

    plot_single_feature(pep_name, df_long, sample_annotation,
      order_col = "order", sample_id_col = "FullRunName",
      batch_col = "MS_batch", measure_col = "Intensity",
      feature_id_col = "peptide_group_label", geom = c("point", "line"),
      color_by_batch = FALSE, color_scheme = "brewer",
      facet_by_batch = FALSE, color_by_col = NULL, color_by_value = NULL,
      plot_title = NULL, vline_color = "red", theme = "classic")

### Arguments

`pep_name` | name of the peptide for diagnostic profiling
`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)
`order_col` | column in `sample_annotation` that determines sample order. It is used for certain diagnostics and normalisations.
`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.
`geom` | whether to show the feature as points and/or connect by lines
`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
`vline_color` | color of vertical lines, typically denoting different MS batches in ordered runs; should be `NULL` for experiments without intrinsic order
`theme` | plot theme (default is 'classical'; other options not implemented)

### Value

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

### See Also

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

### Examples

    single_feature_plot <- plot_single_feature(
    pep_name = "46213_NVGVSFYADKPEVTQEQK_2",
    df_long = example_proteome, example_sample_annotation,
    color_by_col = NULL)

[Package proBatch version 1.0.0 Index]