rna.plot_heatmap: Plots a heatmap of the differentially expressed genes

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

Plots a heatmap of the differentially expressed genes

Description

Plots a heatmap of the differentially expressed genes

Usage

rna.plot_heatmap(
  dds,
  type = c("centered", "contrast"),
  contrast = NULL,
  show_all = TRUE,
  pal = "RdBu",
  kmeans = FALSE,
  k = 6,
  col_limit = NA,
  indicate = NULL,
  clustering_distance = c("euclidean", "maximum", "manhattan", "canberra", "binary",
    "minkowski", "pearson", "spearman", "kendall", "gower"),
  show_row_names = FALSE,
  row_font_size = 6,
  col_font_size = 10,
  plot = TRUE,
  export = TRUE,
  ...
)

Arguments

dds	A DESeqDataSet object containing the normalized gene abundances and the associated metadata
type	Type of heatmap to plot. Either "centered" or "contrast".
contrast	(String or vector of strings) Analyze only significant genes contained in the specified contrast(s). Default is NULL. Contrasts must be given in the form "ConditionA_vs_ConditionB"
show_all	Show gene abundances of all conditions or only of those in the specified constrast(s). Default is TRUE
pal	Color palette to use. Default is "RdBu"
kmeans	Perform k-means clustering on the rows. Default is FALSE
k	Number of clusters to use when kmeans is TRUE. Default is 6
col_limit	Specify a custom range for the color scale of the heatmap. Default is NA, in which case the minimum and maximum of the color scale are calculated as the 5% and 95% percentiles.
indicate	Annotate the heatmap with the specified column from the metadata.
clustering_distance	Distance metric used for clustering. Default is "euclidean".
show_row_names	Show the gene names on the left side of the heatmap. Default is FALSE.
row_font_size	Font size for the gene names. Default is 6
col_font_size	Font size for the condition names. Default is 10
plot	Plot the heatmap. Default is TRUE
export	Export the heatmap as pdf and png. Default is TRUE
...	Other parameters passed to the ComplexHeatmap::Heatmap function

Value

(Invisibly) returns a data frame with the genes and the normalized abundances

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