plot_sample_mean_or_boxplot {proBatch} | R Documentation

## Plot per-sample mean or boxplots for initial assessment

### Description

Plot per-sample mean or boxplots (showing median and quantiles). In ordered samples, e.g. consecutive MS runs, order-associated effects are visualised.

### Usage

    plot_sample_mean(
      data_matrix,
      sample_annotation = NULL,
      sample_id_col = "FullRunName",
      batch_col = "MS_batch",
      color_by_batch = FALSE,
      color_scheme = "brewer",
      order_col = "order",
      vline_color = "grey",
      facet_col = NULL,
      filename = NULL,
      width = NA,
      height = NA,
      units = c("cm", "in", "mm"),
      plot_title = NULL,
      theme = "classic",
      ylimits = NULL
    )

    plot_boxplot(
      df_long,
      sample_annotation = NULL,
      sample_id_col = "FullRunName",
      measure_col = "Intensity",
      batch_col = "MS_batch",
      color_by_batch = TRUE,
      color_scheme = "brewer",
      order_col = "order",
      facet_col = NULL,
      filename = NULL,
      width = NA,
      height = NA,
      units = c("cm", "in", "mm"),
      plot_title = NULL,
      theme = "classic",
      ylimits = NULL,
      outliers = TRUE
    )

### 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")`
`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).
`color_by_batch` | (logical) whether to color points and connecting lines by batch factor as defined by `batch_col`.
`color_scheme` | named vector, names corresponding to unique batch values of `batch_col` in `sample_annotation`. Best created with sample_annotation_to_colors
`order_col` | column in `sample_annotation` that determines sample order. It is used for in initial assessment plots (plot_sample_mean_or_boxplot) and feature-level diagnostics (feature_level_diagnostics). Can be 'NULL' if sample order is irrelevant (e.g. in genomic experiments). For more details, order definition/inference, see define_sample_order and date_to_sample_order
`vline_color` | color of vertical lines, typically denoting different MS batches in ordered runs; should be `NULL` for experiments without intrinsic order
`facet_col` | column in `sample_annotation` with a batch factor to separate plots into facets; usually 2nd to `batch_col`. Most meaningful for multi-instrument MS experiments (where each instrument has its own order-associated effects (see `order_col`) or simultaneous examination of two batch factors (e.g. preparation day and measurement day). For single-instrument case should be set to 'NULL'
`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))
`theme` | ggplot theme, by default `classic`. Can be easily overriden
`ylimits` | range of y-axis to compare two plots side by side, if required.
`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). See `help("example_proteome")` for more details.
`measure_col` | if `df_long` is among the parameters, it is the column with expression/abundance/intensity; otherwise, it is used internally for consistency.
`outliers` | keep (default) or remove the boxplot outliers

### Details

functions for quick visual assessment of trends associated, overall or specific covariate-associated (see `batch_col` and `facet_col`)

### Value

ggplot2 class object. Thus, all aesthetics can be overridden

### See Also

`ggplot`, date_to_sample_order

### Examples

    mean_plot <- plot_sample_mean(example_proteome_matrix, example_sample_annotation,
    order_col = 'order', batch_col = "MS_batch")

    color_list <- sample_annotation_to_colors (example_sample_annotation,
    factor_columns = c('MS_batch'),
    numeric_columns = c('DateTime', 'order'))
    plot_sample_mean(example_proteome_matrix, example_sample_annotation,
    order_col = 'order', batch_col = "MS_batch", color_by_batch = TRUE,
    color_scheme = color_list[["MS_batch"]])

    ## Not run:
    mean_plot <- plot_sample_mean(example_proteome_matrix,
                                  example_sample_annotation,
                                  order_col = 'order', batch_col = "MS_batch",
                                  filename = 'test_meanplot.png',
                                  width = 28, height = 18, units = 'cm')

    ## End(Not run)

    boxplot <- plot_boxplot(log_transform_df(example_proteome),
    sample_annotation = example_sample_annotation,
    batch_col = "MS_batch")

    color_list <- sample_annotation_to_colors (example_sample_annotation,
    factor_columns = c('MS_batch'),
    numeric_columns = c('DateTime', 'order'))
    plot_boxplot(log_transform_df(example_proteome),
    sample_annotation = example_sample_annotation,
    batch_col = "MS_batch", color_scheme = color_list[["MS_batch"]])

    ## Not run:
    boxplot <- plot_boxplot(log_transform_df(example_proteome),
    sample_annotation = example_sample_annotation,
    batch_col = "MS_batch", filename = 'test_boxplot.png',
    width = 14, height = 9, units = 'in')

    ## End(Not run)

[Package proBatch version 1.10.0 Index]