vis_bar: Bar plots

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

Bar plots

Description

Bar plots

Usage

vis_bar(
  .data,
  .by = NA,
  .meta = NA,
  .errorbars = c(0.025, 0.975),
  .errorbars.off = FALSE,
  .stack = FALSE,
  .points = TRUE,
  .test = TRUE,
  .signif.label.size = 3.5,
  .errorbar.width = 0.2,
  .defgroupby = "Sample",
  .grouping.var = "Group",
  .labs = c("X", "Y"),
  .title = "Barplot (.title argument)",
  .subtitle = "Subtitle (.subtitle argument)",
  .legend = NA,
  .leg.title = "Legend (.leg.title argument)",
  .legend.pos = "right",
  .rotate_x = 90
)

Arguments

.data	Data to visualise.
.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.
.errorbars	A numeric vector of length two with quantiles for error bars on sectors. Disabled if ".errorbars.off" is TRUE.
.errorbars.off	If TRUE then plot CI bars for distances between each group. Disabled if no group passed to the ".by" argument.
.stack	If TRUE and .errorbars.off is TRUE then plot stacked bar plots for each Group or 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.
.errorbar.width	Numeric. Width for error bars.
.defgroupby	A name for the column with sample names.
.grouping.var	A name for the column to group by.
.labs	A character vector of length two specifying names for x-axis and y-axis.
.title	The text for the plot's title.
.subtitle	The text for the plot's subtitle.
.legend	If TRUE then displays a legend, otherwise removes legend from the plot.
.leg.title	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".
.rotate_x	How much the x tick text should be rotated? In angles.

Value

A ggplot2 object.

Examples

vis_bar(data.frame(Sample = c("A", "B", "C"), Value = c(1, 2, 3)))

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