draw_trajectory_heatmap {SCORPIUS}

Draw time-series heatmap

Description

draw_trajectory_heatmap draws a heatmap in which the samples are ranked according their position in an inferred trajectory. In addition, the progression groups and feature modules can be passed along to further enhance the visualisation.

Usage

draw_trajectory_heatmap(
  x,
  time,
  progression_group = NULL,
  modules = NULL,
  show_labels_row = FALSE,
  show_labels_col = FALSE,
  scale_features = TRUE,
  progression_group_palette = NULL,
  ...
)

Arguments

x

A numeric matrix or a data frame with one row per sample and one column per feature.

time

A numeric vector containing the inferred time points of each sample along a trajectory.

progression_group

NULL or a vector (or factor) containing the groupings of the samples (default NULL).

modules

NULL or a data frame as returned by extract_modules.

show_labels_row

TRUE if the labels of the rows are to be plotted (default FALSE).

show_labels_col

TRUE if the labels of the cols are to be plotted (default FALSE).

scale_features

TRUE if the values of each feature is to be scaled (default TRUE).

progression_group_palette

A named vector palette for the progression group.

...

Optional arguments to pheatmap

Value

The output of the pheatmap function.

Examples

## Generate a dataset
dataset <- generate_dataset(num_genes=500, num_samples=300, num_groups=4)
expression <- dataset$expression
space <- reduce_dimensionality(expression, ndim=2)
groups <- dataset$sample_info$group_name
traj <- infer_trajectory(space)
time <- traj$time

gimp <- gene_importances(expression, traj$time, num_permutations = 0, ntree = 10000)
gene_sel <- gimp[1:50,]
expr_sel <- expression[,gene_sel$gene]

## Draw a time series heatmap
draw_trajectory_heatmap(expr_sel, time)

## Also show the progression groupings
draw_trajectory_heatmap(expr_sel, time, progression_group=groups)

## Use a different palette
draw_trajectory_heatmap(
  expr_sel, time, progression_group=groups,
  progression_group_palette = setNames(RColorBrewer::brewer.pal(4, "Set2"), paste0("Group ", 1:4))
)

## Group the genes into modules and visualise the modules in a heatmap
modules <- extract_modules(scale_quantile(expr_sel))
draw_trajectory_heatmap(expr_sel, time, progression_group=groups, modules=modules)