clonal_diversity: Clonal diversity plot

In dunbarlabNIH/barcodetrackR: Functions for Analyzing Cellular Barcoding Data

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"
)

dunbarlabNIH/barcodetrackR documentation built on April 26, 2021, 6:20 p.m.