get_heatmap {ssMutPA}

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
)

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.

Value

No return value

Examples

#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)