plot_CV_distr {proBatch} | R Documentation

## Plot CV distribution to compare various steps of the analysis

### Description

Plot CV distribution to compare various steps of the analysis

### Usage

    plot_CV_distr(
      df_long,
      sample_annotation = NULL,
      feature_id_col = "peptide_group_label",
      sample_id_col = "FullRunName",
      measure_col = "Intensity",
      biospecimen_id_col = "EarTag",
      batch_col = NULL,
      unlog = TRUE,
      log_base = 2,
      offset = 1,
      plot_title = NULL,
      filename = NULL,
      theme = "classic"
    )

### Arguments

`df_long` | as in `df_long` for the rest of the package, but, when it has entries for intensity, represented in `measure_col` for several steps, e.g. raw, normalized, batch corrected data, as seen in column `Step`, then multi-step CV comparison can be carried out.
`sample_annotation` | data frame with: `sample_id_col` (this can be repeated as row names) biological covariates technical covariates (batches etc) . See `help("example_sample_annotation")`
`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.
`sample_id_col` | name of the column in `sample_annotation` table, where the filenames (colnames of the `data_matrix` are found).
`measure_col` | if `df_long` is among the parameters, it is the column with expression/abundance/intensity; otherwise, it is used internally for consistency.
`biospecimen_id_col` | column in `sample_annotation` that defines a unique bio ID, which is usually a combination of conditions or groups. Tip: if such ID is absent, but can be defined from several columns, create new `biospecimen_id` column
`batch_col` | column in `sample_annotation` that should be used for batch comparison (or other, non-batch factor to be mapped to color in plots).
`unlog` | (logical) whether to reverse log transformation of the original data
`log_base` | base of the logarithm for transformation
`offset` | small positive number to prevent 0 conversion to `-Inf`
`plot_title` | title of the plot (e.g., processing step + representation level (fragments, transitions, proteins) + purpose (meanplot/corrplot etc))
`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
`theme` | ggplot theme, by default `classic`. Can be easily overriden

### Value

`ggplot` object with the boxplot of CVs on one or several steps

### Examples

    CV_plot = plot_CV_distr(example_proteome,
    sample_annotation = example_sample_annotation,
    measure_col = 'Intensity', batch_col = 'MS_batch',
    plot_title = NULL, filename = NULL, theme = 'classic')

[Package proBatch version 1.4.0 Index]