clonal_contribution {barcodetrackR} | R Documentation

## Clonal contribution plot

### Description

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.

### Usage

    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
    )

### Arguments

`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.

### Value

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.

### Examples

    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
    )

[Package barcodetrackR version 1.0.0 Index]