Plots a heatmap of the differentially expressed proteins

Usage

prot.plot_heatmap(
  dep,
  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 = FALSE,
  ...
)

Arguments

dep: A SummarizedExperiment object containing the normalized protein abundances and the associated metadata
type: Type of heatmap to plot. Either "centered" or "contrast".
contrast: (String or vector of strings) Analyze only significant proteins contained in the specified contrast(s). Default is NULL. Contrasts must be given in the form "ConditionA_vs_ConditionB"
show_all: Show protein 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 protein names on the left side of the heatmap. Default is FALSE.
row_font_size: Font size for the protein 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 proteins and the normalized abundances