vis_heatmap: Visualisation of matrices and data frames using ggplo2-based...

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

Visualisation of matrices and data frames using ggplo2-based heatmaps

Description

Fast and easy visualisations of matrices or data frames with functions based on the ggplot2 package.

Usage

vis_heatmap(
  .data,
  .text = TRUE,
  .scientific = FALSE,
  .signif.digits = 2,
  .text.size = 4,
  .axis.text.size = NULL,
  .labs = c("Sample", "Sample"),
  .title = "Overlap",
  .leg.title = "Overlap values",
  .legend = TRUE,
  .na.value = NA,
  .transpose = FALSE,
  ...
)

Arguments

.data	Input object: a matrix or a data frame. If matrix: column names and row names (if presented) will be used as names for labs. If data frame: the first column will be used for row names and removed from the data. Other columns will be used for values in the heatmap.
.text	If TRUE then plots values in the heatmap cells. If FALSE does not plot values, just plot coloured cells instead.
.scientific	If TRUE then uses the scientific notation for numbers (e.g., "2.0e+2").
.signif.digits	Number of significant digits to display on plot.
.text.size	Size of text in the cells of heatmap.
.axis.text.size	Size of text on the axis labels.
.labs	A character vector of length two with names for x-axis and y-axis, respectively.
.title	The The text for the plot's title.
.leg.title	The The text for the plots's legend. Provide NULL to remove the legend's title completely.
.legend	If TRUE then displays a legend, otherwise removes the legend from the plot.
.na.value	Replace NA values with this value. By default they remain NA.
.transpose	Logical. If TRUE then switch rows and columns.
...	Other passed arguments.

Value

A ggplot2 object.

See Also

vis, repOverlap.

Examples

data(immdata)
ov <- repOverlap(immdata$data)
vis_heatmap(ov)
gu <- geneUsage(immdata$data, "hs.trbj")
vis_heatmap(gu)

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