clonal_diversity {barcodetrackR} | R Documentation

## Clonal diversity plot

### Description

A line plot that tracks a diversity measure from selected samples of the SummarizedExperiment object plotted over a specified variable.

### Usage

    clonal_diversity(
      your_SE,
      plot_over,
      plot_over_display_choices = NULL,
      keep_numeric = TRUE,
      group_by,
      group_by_choices = NULL,
      index_type = "shannon",
      point_size = 3,
      line_size = 2,
      text_size = 12,
      your_title = NULL,
      return_table = FALSE
    )

### Arguments

`your_SE` | Summarized Experiment object containing clonal tracking data as created by the barcodetrackR 'create_SE' function.
`plot_over` | The column of metadata that you want to be the x-axis of the plot. e.g. timepoint
`plot_over_display_choices` | Choice(s) from the column designated in plot_over that will be used for plotting. Defaults to all if left as NULL.
`keep_numeric` | If plot_over is numeric, whether to space the x-axis appropriately according to the numerical values.
`group_by` | The column of metadata you want to group by e.g. cell_type
`group_by_choices` | Choice(s) from the column designated in group_by that will be used for plotting. Defaults to all if left as NULL.
`index_type` | Character. One of "shannon", "shannon_count", "simpson", or "invsimpson".
`point_size` | Numeric. Size of points.
`line_size` | Numeric. Size of lines.
`text_size` | Numeric. Size of text in plot.
`your_title` | Character. The title for the plot.
`return_table` | Logical. IF set to TRUE, rather than returning the plot of clonal diversity, the function will return a dataframe containing the diversity index values for each specified sample.

### Value

Outputs plot of a diversity measure tracked for groups over a factor. Or if return_table is set to true, a dataframe will be returned instead.

### Examples

    data(wu_subset)
    clonal_diversity(
        your_SE = wu_subset, index_type = "shannon",
        plot_over = "months", group_by = "celltype"
    )

[Package barcodetrackR version 1.0.0 Index]