prot.plot_heatmap_all: Plots a heatmap of all protein abundances

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Plots a heatmap of all protein abundances

Description

Plots a heatmap of all protein abundances

Usage

prot.plot_heatmap_all(
  se,
  show_all = TRUE,
  pal = "RdBu",
  kmeans = FALSE,
  k = 6,
  col_limit = NA,
  indicate = "condition",
  clustering_distance = "euclidean",
  show_row_names = FALSE,
  row_font_size = 6,
  col_font_size = 10,
  plot = TRUE,
  export = TRUE,
  scale = TRUE,
  show_row_dend = FALSE,
  ...
)

Arguments

se	A SummarizedExperiment object
show_all	Logical. Show protein abundances of all conditions or only of those in the specified constrast(s). Default is TRUE
pal	Character. Color palette to use. Default is "RdBu"
kmeans	Logical. Perform kmeans clustering on protein abundances. Default is FALSE
k	Numeric. Number of clusters to use in kmeans clustering. Default is 6
col_limit	Numeric. Maximum intensity for the heatmap. Default is NA
indicate	Character. Column name of the annotation to indicate in the heatmap. Default is "condition"
clustering_distance	Character. Distance metric to use for clustering. Default is "euclidean"
show_row_names	Logical. Show protein names on the left of the heatmap. Default is FALSE
row_font_size	Numeric. Font size for protein names. Default is 6
col_font_size	Numeric. Font size for condition names. Default is 10
plot	Logical. Plot the heatmap or not. Default is TRUE
export	Logical. Export the heatmap to a pdf and png file. Default is TRUE
scale	Logical. Scale the data before plotting. Default is TRUE
show_row_dend	Logical. Show row dendrogram. Default is FALSE
...	Other parameters to pass to ComplexHeatmap::Heatmap

Value

A data frame with protein abundances

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.