immunarch (version 0.10.3)

vis_box: 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"
)

Value

A ggplot2 object.

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 reshape2::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".

See Also

vis.immunr_gene_usage, geneUsage

Examples

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