heatmap_plot: Plots subpathways heatmap

In babelomics/hipathia: HiPathia: High-throughput Pathway Analysis

Plots subpathways heatmap

Description

Plots a heatmap with the values of the subpathways.

Usage

heatmap_plot(
  data,
  group = NULL,
  sel_assay = 1,
  colors = "classic",
  sample_clust = TRUE,
  variable_clust = FALSE,
  labRow = NULL,
  labCol = NULL,
  sample_colors = NULL,
  scale = TRUE,
  save_png = NULL,
  legend = TRUE,
  legend_xy = "topright",
  pch = 15,
  main = NULL
)

Arguments

data	Either a SummarizedExperiment or a matrix with the values to be plotted. Rows are features and columns are samples.
group	Either a character indicating the name of the column in colData including the classes to plot, or a character vector with the class to which each sample belongs. Samples must be ordered as in data. By default, all samples will be assigned to the same class.
sel_assay	Character or integer, indicating the assay to be normalized in the SummarizedExperiment. Default is 1.
colors	Either a character vector with colors or a key name indicating the color scheme to be used in the heatmap. If a character vector is provided, it is recommended to provide at least 3 colors. Three different predefined color schemes may be selected by providing a key name. Options are: * classic Blue for lower values, white for medium values, red for higher values. * hipathia Hipathia predefined color scheme: Green for lower values, white for medium values, orange for higher values. * redgreen Green for lower values, black for medium values, red for higher values. By default classic color scheme is applied.
sample_clust	Boolean, whether to cluster samples (columns). By default TRUE.
variable_clust	Boolean, whether to cluster variables (rows). By default FALSE. If TRUE, rows with 0 variance are removed.
labRow, labCol	Character vectors with row and column labels to be used. By default rownames(data) or colnames(data) are used, respectively.
sample_colors	Named character vector of colors. The names of the colors must be the classes in group. Each sample will be assigned the color corresponding to its class, taken from the group vector. By default a color will be assigned automatically to each class.
scale	Boolean, whether to scale each row to the interval [0,1]. Default is TRUE.
save_png	Path to the file where the image as PNG will be saved. By default, the image is not saved.
legend	Boolean, whether to display a legend.
legend_xy	Position for the legend, in case legend is TRUE.
pch	Graphical parameter from par() function.
main	Main title of the image

Value

Heatmap of the values of the subpathways

Examples

data(brca_design)
data(path_vals)
sample_group <- brca_design[colnames(path_vals),"group"]
heatmap_plot(path_vals, group = sample_group)
heatmap_plot(path_vals, group = "group", colors = "hipathia",
variable_clust = TRUE)

babelomics/hipathia documentation built on July 27, 2022, 2:23 p.m.