vis_box: Flexible box-plots for visualisation of distributions

In immunomind/immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

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)

immunomind/immunarch documentation built on March 20, 2024, 12:01 p.m.