clonal_count {barcodetrackR} | R Documentation

## Clonal count plot

### Description

A line plot that tracks the total number of clones or the cumulative number of clones from selected samples of the SummarizedExperiment object plotted over a specified variable.

### Usage

    clonal_count(
      your_SE,
      percent_threshold = 0,
      plot_over,
      plot_over_display_choices = NULL,
      keep_numeric = TRUE,
      group_by,
      group_by_choices = NULL,
      cumulative = FALSE,
      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.
`percent_threshold` | Numeric. The percent threshold for which to count barcodes as present or not present. Set to 0 by default.
`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.
`cumulative` | Logical. If TRUE, will plot cumulative counts over the 'plot_over' argument rather than unique counts per sample (the default, which is FALSE).
`point_size` | Numeric. Size of points.
`line_size` | Numeric. Size of lines.
`text_size` | Numeric. Size of text in plot.
`your_title` | The title for the plot.
`return_table` | Logical. If set to true, rather than returning a plot, the function will return the clonal count or cumulative count of each sample in a dataframe.

### Value

Outputs plot of a diversity measure tracked for groups over a factor. Or if return_table is set to TRUE, a dataframe of the number of clones (or cumulative clones) for each sample.

### Examples

    data(wu_subset)
    clonal_count(your_SE = wu_subset, cumulative = FALSE, plot_over = "months", group_by = "celltype")

[Package barcodetrackR version 1.0.0 Index]