get_heatmap: Plotting a heatmap with subtype labels.

Description

The function `get_heatmap` is used to plot a heatmap with subtype labels.

Usage

get_heatmap(
  Path_ES,
  Path_name,
  samp_class,
  scale = "row",
  cluster_rows = TRUE,
  cluster_cols = FALSE,
  show_rownames = TRUE,
  show_colnames = FALSE,
  fontsize = 8,
  annotation_legend = TRUE,
  annotation_names_row = TRUE,
  annotation_names_col = TRUE
)

Value

A heatmap

Arguments

Path_ES: Single-sample mutation-based pathway enrichment score profiles.The file can be generated by the function `get_RWR_ES`.
Path_name: The names of the pathways that you want to show in the heatmap.The Path_name must be included in the row names of the Path_ES .
samp_class: A vector containing information about the subtype labels.The vector can be generated by the function `get_samp_class`.
scale: character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none".
cluster_rows: Boolean values determining if rows should be clustered or hclust object.
cluster_cols: Boolean values determining if columns should be clustered or hclust object.
show_rownames: Boolean specifying if row names are be shown.
show_colnames: Boolean specifying if column names are be shown.
fontsize: base font size for the plot.
annotation_legend: Boolean value showing if the legend for annotation tracks should be drawn .
annotation_names_row: Boolean value showing if the names for row annotation tracks should be drawn.
annotation_names_col: Boolean value showing if the names for column annotation tracks should be drawn.

Examples

Run this code

#load the data
data(Path_ES,sample_class,Path_Name)
#perform the function `get_heatmap`.
get_heatmap(Path_ES,Path_name=Path_Name,samp_class=sample_class)

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