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Plotting

Plotting a cell_state_graph

The function plot_annotations():

  • cell_state_graph
  • color_nodes_by
  • label_nodes_by
plot_annotations(notochord_state_graph, node_size = 4.5)

The function plot_abundance_changes():

  • cell_state_graph
  • comp_abund_table

To see how to run Hooke to make a comp_abund_table, see our differential abundance page.

plot_abundance_changes(notochord_state_graph, lmx_fc %>% filter(timepoint_x==60),  node_size = 4.5)

The function plot_gene_expr:

  • cell_state_graph
  • genes - a list of genes to plot
  • aggregate - whether to sum the genes in the genes list
plot_gene_expr(notochord_state_graph, genes=c("lmx1bb", "lmx1ba")) 


plot_gene_expr(notochord_state_graph, genes=c("lmx1bb", "lmx1ba"), aggregate = T)

The function plot_degs:

  • cell_state_graph
  • deg_table

To see how to run DEGs to make a deg_table, see our DEG page.

plot_degs(notochord_state_graph, lmx1b_degs %>% filter(gene_short_name == "col2a1a"), node_size = 4.5, fc_limits = c(-1,1))