bias_lineplot {barcodetrackR} | R Documentation

## Bias line plot

### Description

Given a summarized experiment and a specified factor to compare bias between "split_bias_on", shows the value of that bias plotted against another specified factor "split_bias_over" where each clone is represented by a line shaded by its overall abundance in the two samples being compared.

### Usage

    bias_lineplot(
      your_SE,
      split_bias_on,
      bias_1,
      bias_2,
      split_bias_over,
      bias_over = NULL,
      remove_unique = FALSE,
      text_size = 16,
      keep_numeric = TRUE,
      return_table = FALSE
    )

### Arguments

`your_SE` | SummarizedExperiment of barcode data and associated metadata
`split_bias_on` | The column of metadata corresponding to cell types (or other factor to be compared.)
`bias_1` | The first cell type (or other factor) to be compared. Must be a possible value of the split_bias_on column of your metadata. Will be on the UPPER side of the line plot
`bias_2` | The second cell type (or other factor) to be compared. Must be a possible value of the split_bias_on column of your metadata. Will be on the LOWER side of the line plot
`split_bias_over` | The column of metadata to plot by. If numeric, y axis will be in increasing order. If categorical, it will follow order of metadata.
`bias_over` | Choice(s) from the column designated in 'split_bias_over' that will be used for plotting. Defaults to all.
`remove_unique` | Logical. If set to true, only clones present in both samples will be considered.
`text_size` | Numeric. The size of the text in the plot.
`keep_numeric` | Logical. Whether to keep the numeric spacing within split_bias_over or switch to discrete x scale.
`return_table` | Logical. If set to TRUE, rather than returnign a plot, the function will return a dataframe containing for each barcode sequence and each point of comparison: the bias value, the added proportion between the two factors at that point (cumul_sum), and the maximum cumul_sum (peak_abundance) of that barcode sequence at any point of comparison.

### Value

Bias line plot for two lineages over time. Or if return_table is set to TRUE, a dataframe containing the bias values for each barcode sequence between the two samples at all points of comparison.

### Examples

    data(wu_subset)
    bias_lineplot(
        your_SE = wu_subset, split_bias_on = "celltype",
        bias_1 = "B", bias_2 = "T", split_bias_over = "months"
    )

[Package barcodetrackR version 1.0.0 Index]