plot_hierarchical_clustering {proBatch} | R Documentation

## cluster the data matrix to visually inspect which confounder dominates

### Description

cluster the data matrix to visually inspect which confounder dominates

### Usage

    plot_hierarchical_clustering(
      data_matrix,
      sample_annotation,
      sample_id_col = "FullRunName",
      color_list = NULL,
      factors_to_plot = NULL,
      fill_the_missing = 0,
      distance = "euclidean",
      agglomeration = "complete",
      label_samples = TRUE,
      label_font = 0.2,
      filename = NULL,
      width = 38,
      height = 25,
      units = c("cm", "in", "mm"),
      plot_title = NULL,
      ...
    )

### 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).
`color_list` | list, as returned by `sample_annotation_to_colors`, where each item contains a color vector for each factor to be mapped to the color.
`factors_to_plot` | vector of technical and biological covariates to be plotted in this diagnostic plot (assumed to be present in `sample_annotation`)
`fill_the_missing` | numeric value determining how missing values should be substituted. If `NULL`, features with missing values are excluded.
`distance` | distance metric used for clustering
`agglomeration` | agglomeration methods as used by `hclust`
`label_samples` | if `TRUE` sample IDs (column names of `data_matrix`) will be printed
`label_font` | size of the font. Is active if `label_samples` is `TRUE`, ignored otherwise
`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))
`...` | other parameters of `plotDendroAndColors` from `WGCNA` package

### Value

No return

### See Also

`hclust`, `sample_annotation_to_colors`, `plotDendroAndColors`

### Examples

    selected_batches = example_sample_annotation$MS_batch %in%
                                                  c('Batch_1', 'Batch_2')
    selected_samples = example_sample_annotation$FullRunName[selected_batches]
    test_matrix = example_proteome_matrix[,selected_samples]

    hierarchical_clustering_plot <- plot_hierarchical_clustering(
    example_proteome_matrix, example_sample_annotation,
    factors_to_plot = c('MS_batch', 'Diet', 'DateTime'),
    color_list = NULL,
    distance = "euclidean", agglomeration = 'complete',
    label_samples = FALSE)

    #with defined color scheme:
    color_list <- sample_annotation_to_colors (example_sample_annotation,
    factor_columns = c('MS_batch', "Strain", "Diet", "digestion_batch"),
    numeric_columns = c('DateTime', 'order'))
    hierarchical_clustering_plot <- plot_hierarchical_clustering(
    example_proteome_matrix, example_sample_annotation,
    factors_to_plot = c('MS_batch', "Strain", 'DateTime', "digestion_batch"),
    color_list = color_list,
    distance = "euclidean", agglomeration = 'complete',
    label_samples = FALSE)

[Package proBatch version 1.11.0 Index]