make_heatmap: Make a Heatmap using ComplexHeatmap package.

In ShinyFabio/ADViSELipidomics: Shinyapp for the acquisition and the analysis of lipidomics data

Make a Heatmap using ComplexHeatmap package.

Description

This function render a Heatmap using ComplexHeatmap package.

Usage

make_heatmap(
  data,
  add_rowannot = "Product_Batch",
  add_colannot = "Class",
  log_data = FALSE,
  scale_data = "column",
  order_data = TRUE,
  row_dend = TRUE,
  row_nclust = 2,
  col_dend = TRUE,
  col_nclust = 3,
  dist_method = "euclidean",
  clust_method = "ward.D2",
  col_lab = "Lipids",
  unit_legend = "ug/ml",
  col_label_size = 8,
  padding = c(2, 2, 2, 15)
)

Arguments

data	A summarizedexperiment object. Tested only on sumexp averaged
add_rowannot	A column used for the left (row) annotation (e.g. "Product_Batch")
add_colannot	A column used for the bottom (column) annotation (e.g. "Class")
log_data	Logical value. Set to TRUE to perform a log2 scaling.
scale_data	Scaling data option. Data can be scaled (using scale()) by row ("row"), by column ("column") or not scaled ("none"). The result is the z-score.
order_data	Logical value. Set to TRUE if you want to performin the ordering based on the add_rowannot value.
row_dend	Boolean. Render dendogram on rows (TRUE or FALSE).
row_nclust	Numeric. Number of cluster in the row dendrogram.
col_dend	Boolean. Render dendogram on columns (TRUE or FALSE).
col_nclust	Numeric. Number of cluster in the column dendrogram.
dist_method	Choose a distance method (e.g "euclidean"). See ?stats::dist().
clust_method	Choose a clustering method (e.g "ward.D"). See ?stats::hclust().
col_lab	A label for the column (i.e. "Lipids").
unit_legend	An unit label for the legend. If data are scaled will be "Z-score" otherwise will be the input.
col_label_size	Size of the column labels. By default col_label_size = 10.
padding	padding for the heatmap in mm. By default padding = c(2,2,2,15).

ShinyFabio/ADViSELipidomics documentation built on March 21, 2023, 7:30 a.m.