prot.plot_heatmap: Plots a heatmap of the differentially expressed proteins

prot.plot_heatmapR Documentation

Plots a heatmap of the differentially expressed proteins

Description

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 = TRUE,
  ...
)

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


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