plot_sample_corr_distribution {proBatch} | R Documentation

## Create violin plot of sample correlation distribution

### Description

Useful to visualize within batch vs within replicate vs non-related sample correlation

### Usage

    plot_sample_corr_distribution(data_matrix, sample_annotation,
      repeated_samples = NULL, sample_id_col = "FullRunName",
      batch_col = "MS_batch", biospecimen_id_col = "EarTag",
      filename = NULL, width = NA, height = NA, units = c("cm", "in",
      "mm"), plot_title = "Sample correlation distribution",
      plot_param = "batch_replicate", theme = "classic")

    plot_sample_corr_distribution.corrDF(corr_distribution, filename = NULL,
      width = NA, height = NA, units = c("cm", "in", "mm"),
      plot_title = "Sample correlation distribution",
      plot_param = "batch_replicate", 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")`)
`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")`
`repeated_samples` | if `NULL`, correlation of all samples is plotted
`sample_id_col` | name of the column in `sample_annotation` table, where the filenames (colnames of the `data_matrix` are found).
`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).
`biospecimen_id_col` | column in `sample_annotation` that captures the biological sample, that (possibly) was profiled several times as technical replicates. Tip: if such ID is absent, but can be defined from several columns, create new `biospecimen_id` column
`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))
`plot_param` | columns, defined in correlation_df, which is output of `calculate_sample_corr_distr`, specifically, `replicate` `batch_the_same` `batch_replicate` `batches`
`theme` | ggplot theme, by default `classic`. Can be easily overriden
`corr_distribution` | data frame with correlation distribution, as returned by `calculate_sample_corr_distr`

### Value

`ggplot` type object with violin plot for each `plot_param`

### See Also

`calculate_sample_corr_distr`, `ggplot`

### Examples

    sample_corr_distribution_plot <- plot_sample_corr_distribution(
    example_proteome_matrix,
    example_sample_annotation, batch_col = 'MS_batch',
    biospecimen_id_col = "EarTag",
    plot_param = 'batch_replicate')

    corr_distribution = calculate_sample_corr_distr(data_matrix = example_proteome_matrix,
    sample_annotation = example_sample_annotation,
    batch_col = 'MS_batch',biospecimen_id_col = "EarTag")
    sample_corr_distribution_plot <- plot_sample_corr_distribution.corrDF(corr_distribution,
    plot_param = 'batch_replicate')

    ## Not run:
    sample_corr_distribution_plot <- plot_sample_corr_distribution.corrDF(corr_distribution,
    plot_param = 'batch_replicate',
    filename = 'test_sampleCorr.png',
    width = 28, height = 28, units = 'cm')

    ## End(Not run)

[Package proBatch version 1.3.0 Index]