dist_plot {barcodetrackR} | R Documentation

## Pairwise Distance Plot

### Description

Plots the pairwise distances of the specified assay between each sample-sample pair in the provided SummarizedExperiment.

### Usage

    dist_plot(
      your_SE,
      assay = "proportions",
      plot_labels = colnames(your_SE),
      dist_method = "euclidean",
      cluster_tree = FALSE,
      your_title = "",
      grid = TRUE,
      label_size = 10,
      plot_type = "color",
      no_negatives = FALSE,
      return_table = FALSE,
      color_pal = "Blues",
      number_size = 3,
      point_scale = 5,
      minkowski_p = 2
    )

### Arguments

`your_SE` | A Summarized Experiment object.
`assay` | The choice of assay to use for the correlation calculation. Set to "proportions" by default.
`plot_labels` | Vector of x axis labels. Defaults to colnames(your_SE).
`dist_method` | Character. Distance OR similarity measure from the 'proxy' package. Full list of distance and similarity measures can be found using 'summary(proxy::pr_DB)'. Default is "euclidean". Distances will be calculated for distance measures, while similarities will be calculated for similarity measures. Distance OR similarity measure will be calculated using the 'assay' specified.
`cluster_tree` | Logical. Whether to cluster samples and plot a hierarchical tree calculated from the distance or similarity measure used. Default is FALSE.
`your_title` | Character. The title for the plot.
`grid` | Logical. Include a grid or not in the resulting plot.
`label_size` | Numeric. The size of the column labels.
`plot_type` | Character. One of "color", "circle", or "number".
`no_negatives` | Logical. Whether to make negative correlations = 0.
`return_table` | Logical. Whether or not to return table of p-values, confidence intervals, and R values instead of displaying a plot.
`color_pal` | Character. One of 'Reds', 'Purples', 'Oranges', 'Greys', 'Greens', or 'Blues' that designates the brewer.pal color scale to use.
`number_size` | Numeric. size of the text label when plot_type is "number".
`point_scale` | Numeric. The size of the largest point if the plot_type is "circle".
`minkowski_p` | Numeric. If 'Minkowski' is chosen, the 'p' used to calculate the Minkowski distance.

### Value

Plots pairwise correlation plot for the samples in your_SE.

### Examples

    data(wu_subset)
    dist_plot(your_SE = wu_subset, plot_type = "color")
    # "

[Package barcodetrackR version 1.0.0 Index]