Get started

The single cell objects can be explored in R using the Monocle3, Hooke, and Platt. They contain UMAP coordinates for immediate plotting of your favorite genes, time points, or genetic perturbations. For help with more in-depth custom analyses, please visit the package tutorials.

Loading and subsetting the data

library(monocle3)
library(hooke)
library(tidyverse)


# load the reference

ref_cds = load_monocle_objects("reference_cds")

hooke:::my_plot_cells(ref_cds, color_cells_by = "tissue")

To switch to the sub-UMAP partition space:

ref_cds = hooke:::switch_reducedDims(ref_cds, umap_space = "sub_UMAP")

hooke:::my_plot_cells(ref_cds, color_cells_by = "projection_group") + facet_wrap(~projection_group)

You can subset the data by partition as follows:

# subset the data by projection group
notochord_cds = ref_cds[,colData(ref_cds)$projection_group == "notochord"]

hooke:::my_plot_cells(notochord_cds, color_cells_by = "cell_type")

Reference graphs

ref_graphs = readRDS("combined_state_graph.rds")

ref_ccs = new_cell_count_set(ref_cds, sample_group = "embryo", cell_group = "cell_type")

ref_csg = new_cell_state_graph(ref_graphs, ref_ccs, num_layers = 3)

platt:::plot_annotations(ref_csg, color_nodes_by = "projection_group")