plot_heatmap: Plot a heatmap of qvals from SCPA

In jackbibby1/SCPA: Single Cell Pathway Analysis

Plot a heatmap of qvals from SCPA

Description

This function takes the output from SCPA and plots a heatmap of the qvals

Usage

plot_heatmap(
  scpa_out,
  highlight_pathways = NULL,
  row_fontsize = 6,
  column_fontsize = 10,
  column_names = colnames(scpa_out),
  show_row_names = TRUE,
  cluster_columns = TRUE,
  hm_colors = NULL,
  scale_breaks = NULL
)

Arguments

scpa_out	Data frame that contains a "Pathway" column, and a column or multiple columns containing qvals. This can be the direct output from compare_pathways(), or a custom data frame.
highlight_pathways	Pathway or pathways to annotate on the heatmap, supplied as character vector. If no argument is given, all pathways are shown
row_fontsize	Font size of pathway names
column_fontsize	Font size of the sample names
column_names	Option to supply names of the heatmap columns if more than one populations is present
show_row_names	Should row names be shown in the heatmap?
cluster_columns	Should columns in the heatmap be clustered?
hm_colors	Colors to be used in the heatmap
scale_breaks	Breaks to be used in the colors of the heatmap. Length must be equal to the number of colors.

Value

list of pathways with corresponding genes

Examples

## Not run: 
plot_heatmap(
     scpa_out = scpa_result,
     pathway = "mtorc"
)

## End(Not run)

jackbibby1/SCPA documentation built on May 14, 2024, 7:16 a.m.