clonal_contribution: Clonal contribution plot
In d93espinoza/barcodetrackR: Functions for Analyzing Cellular Barcoding Data

Description Usage Arguments Value Examples

Bar or line plot of percentage contribution of the top clones from a selected sample or all clones across samples matching the specified filter within the SummarizedExperiment object. Usually used for tracking a cell lineage's top clones over time.

clonal_contribution(
  your_SE,
  SAMPLENAME_choice = NULL,
  filter_by,
  filter_selection,
  plot_over,
  plot_over_display_choices = NULL,
  clone_sequences = NULL,
  n_clones = 10,
  graph_type = "bar",
  keep_numeric = TRUE,
  plot_non_selected = TRUE,
  linesize = 0.2,
  text_size = 15,
  your_title = "",
  y_limit = NULL,
  return_table = FALSE
)

`your_SE`	A Summarized Experiment object.
`SAMPLENAME_choice`	The identifying SAMPLENAME from which to obtain the top "n_clones" clones to color. If NULL and clone_sequences is NULL, all clones will be shown as gray.
`filter_by`	Name of metadata column to filter by e.g. Lineage
`filter_selection`	The value of the filter column to display e.g. "T" (within Lineage)
`plot_over`	The column of metadata that you want to be the x-axis of the plot. e.g. Month. For numeric metadata, the x-axis will be ordered in ascending fashion. For categorical metadata, the sample order will be followed.
`plot_over_display_choices`	Choice(s) from the column designated in plot_over that will be used for plotting. Defaults to all.
`clone_sequences`	The identifying rownames within your_SE for which to plot. SAMPLENAME_choice should be set to NULL or not specified if clone_sequences is specified.
`n_clones`	Numeric. Number of top clones from SAMPLENAME_choice that should be assigned a unique color.
`graph_type`	Choice of "bar" or "line" for how to display the clonal contribution data
`keep_numeric`	If plot_over is numeric, whether to space the x-axis appropriately according to the numerical values.
`plot_non_selected`	Plot clones NOT found within the top clones in SAMPLENAME_choice or the specified clones passed to clone_sequences. These clones are colored gray. If both SAMPLENAME_choice and clone_sequences are NULL, this argument must be set to TRUE. Otherwise, there will be no data to show.
`linesize`	Numeric. Thickness of the lines.
`text_size`	Numeric. Size of text in plot.
`your_title`	Title string for your plot.
`y_limit`	Numeric. What the max value of the y scale should be for the "proportions" assay.
`return_table`	Logical. If set to TRUE, the function will return a dataframe with each sequence that is selected and its percentage contribution to each selected sample rather than a plot.

Displays a stacked area line or bar plot (made by ggplot2) of the samples' top clones. Or, if return_table is set to TRUE, returns a dataframe of the percentage abundances in each sample.

data(wu_subset)
clonal_contribution(
    your_SE = wu_subset, graph_type = "bar",
    SAMPLENAME_choice = "ZJ31_20m_T",
    filter_by = "celltype", filter_selection = "T",
    plot_over = "months", n_clones = 10
)