script.R

In dynverse/dynplot2: Grammar of graphics for single-cell data

library(dyntoy)
library(tidyverse)
library(dynwrap)

dataset <- generate_dataset(model = "bifurcating", num_cells = 1000, add_prior_information = F, add_velocity = T, allow_tented_progressions = FALSE)
dataset <- dataset %>% add_dimred(dimred = dyndimred::dimred_landmark_mds) %>% add_root()

dynplot(dataset) +
  geom_cell_point(aes(colour = select_expression("G1"))) +
  scale_expression_fillcolour() + # a scale has to be given here, otherwise error
  new_scale_fillcolour() +
  geom_trajectory_segments(aes(colour = milestone_percentages), size = 2) +
  geom_milestone_label(aes(fill = milestone_id)) +
  scale_milestones_fillcolour()


dynplot(dataset) +
  geom_cell_point(color = "grey80") +
  new_scale_fillcolour() +
  geom_trajectory_segments(aes(colour = milestone_percentages), size = 2) +
  geom_milestone_label(aes(fill = milestone_id)) +
  scale_milestones_fillcolour() +
  geom_velocity_arrow(stat = stat_velocity_grid(grid_n = 20))

dynplot(dataset, layout = layout_graph(dataset)) +
  geom_trajectory_divergence() +
  geom_trajectory_segments(size = 3, color = "#333333") +
  geom_cell_point(aes(colour = select_expression("G1"))) +
  scale_expression_fillcolour() +
  new_scale_fillcolour() +
  geom_cell_point(aes(colour = milestone_percentages)) +
  geom_milestone_label(aes(fill = milestone_id)) +
  scale_milestones_fillcolour()


dynplot(dataset, layout = layout_onedim(dataset, equal_cell_width = TRUE, margin = 0.05)) +
  geom_trajectory_segments(aes(color = milestone_percentages), size = 5, color = "#333333") +
  geom_trajectory_connection() +
  scale_milestones_fillcolour() +
  new_scale_fillcolour() +
  geom_cell_point(aes(colour = select_expression("G2"))) +
  scale_expression_fillcolour() +
  new_scale_fillcolour() +
  # geom_cell_point(aes(colour = milestone_percentages)) +
  geom_milestone_label(aes(y = -0.1, fill = milestone_id, hjust = as.integer(type == "end"))) +
  scale_milestones_fillcolour()





dynplot(dataset, layout = layout_dendro(dataset)) +
  geom_trajectory_segments(aes(color = milestone_percentages), size = 5, color = "#333333") +
  geom_trajectory_connection() +
  scale_milestones_fillcolour() +
  new_scale_fillcolour() +
  geom_cell_point(aes(colour = select_expression("G1"))) +
  scale_expression_fillcolour() +
  new_scale_fillcolour() +
  # geom_cell_point(aes(colour = milestone_percentages)) +
  geom_milestone_label(aes(fill = milestone_id)) +
  scale_milestones_fillcolour()



dynplot(dataset, layout = layout_dendro(dataset)) +
  geom_trajectory_segments(aes(color = milestone_percentages), size = 5, color = "#333333") +
  geom_trajectory_connection() +
  scale_milestones_fillcolour() +
  new_scale_fillcolour() +
  geom_cell_point(aes(y = y + dynutils::scale_minmax(select_expression("G2")) * 0.5 - 0.25, colour = select_expression("G2"))) +
  scale_expression_fillcolour() +
  new_scale_fillcolour() +
  # geom_cell_point(aes(colour = milestone_percentages)) +
  geom_milestone_label(aes(fill = milestone_id)) +
  scale_milestones_fillcolour()










cell_layout <- layout_onedim(dataset)
feature_modules <- get_features(dataset)
feature_layout <- layout_modules(dataset, feature_modules = feature_modules, cell_layout = cell_layout)
layout <- layout_heatmap(dataset, feature_layout = feature_layout)

dynplot(dataset, layout = layout) +
  geom_trajectory_segments(aes(color = milestone_percentages)) +
  geom_trajectory_connection() +
  geom_milestone_label(aes(fill = milestone_id, hjust = as.integer(type == "end"))) +
  scale_milestones_fillcolour() +
  new_scale_fillcolour() +
  geom_expression_raster() +
  scale_expression_fillcolour() +
  new_scale_fillcolour() +
  geom_tile(aes(x = x, y = 1))