clonal_count: Clonal count plot
In d93espinoza/barcodetrackR: Functions for Analyzing Cellular Barcoding Data

Description Usage Arguments Value Examples

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.

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
)

`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.

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.