Plot a heatmap of qvals from SCPA — plot_heatmap • Single Cell Pathway Analysis (SCPA)

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

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

if (FALSE) {
plot_heatmap(
     scpa_out = scpa_result,
     pathway = "mtorc"
)
}