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)