R: Flexible box-plots for visualisation of distributions

vis_box {immunarch} | R Documentation

## Flexible box-plots for visualisation of distributions

### Description

Visualisation of distributions using ggplot2-based boxplots.

### Usage

    vis_box(
      .data,
      .by = NA,
      .meta = NA,
      .melt = TRUE,
      .points = TRUE,
      .test = TRUE,
      .signif.label.size = 3.5,
      .defgroupby = "Sample",
      .grouping.var = "Group",
      .labs = c("X", "Y"),
      .title = "Boxplot (.title argument)",
      .subtitle = "Subtitle (.subtitle argument)",
      .legend = NA,
      .leg.title = "Legend (.leg.title argument)",
      .legend.pos = "right"
    )

### Arguments

`.data` | Input matrix or data frame.
`.by` | Pass NA if you want to plot samples without grouping. You can pass a character vector with one or several column names from ".meta" to group your data before plotting. In this case you should provide ".meta". You can pass a character vector that exactly matches the number of samples in your data, each value should correspond to a sample's property. It will be used to group data based on the values provided. Note that in this case you should pass NA to ".meta".
`.meta` | A metadata object. An R dataframe with sample names and their properties, such as age, serostatus or hla.
`.melt` | If TRUE then apply melt to the ".data" before plotting. In this case ".data" is supposed to be a data frame with the first character column reserved for names of genes and other numeric columns reserved to counts or frequencies of genes. Each numeric column should be associated with a specific repertoire sample.
`.points` | A logical value defining whether points will be visualised or not.
`.test` | A logical vector whether statistical tests should be applied. See "Details" for more information.
`.signif.label.size` | An integer value defining the size of text for p-value.
`.defgroupby` | A name for the column with sample names.
`.grouping.var` | A name for the column to group by.
`.labs` | Character vector of length two with names for x-axis and y-axis, respectively.
`.title` | The text for the title of the plot.
`.subtitle` | The The text for the plot's subtitle.
`.legend` | If TRUE then displays a legend, otherwise removes legend from the plot.
`.leg.title` | The The text for the plots's legend. Provide NULL to remove the legend's title completely.
`.legend.pos` | Positions of the legend: either "top", "bottom", "left" or "right".

### Value

A ggplot2 object.

### See Also

vis.immunr_gene_usage, geneUsage

### Examples

    vis_box(data.frame(Sample = sample(c("A", "B", "C"), 100, TRUE), Value = rnorm(100)), .melt = FALSE)

[Package immunarch version 0.6.5 Index]