> Reference > > dynplot :: Plot a trajectory > Plot the expression across a trajectory in a heatmap

Plot the expression across a trajectory in a heatmap

When using RStudio: the heatmap will not show inside the plot area, but will be visible once you click the zoom button.

plot_heatmap(trajectory, expression_source = "expression",
  features_oi = 20, clust = "ward.D2", margin = 0.02,
  color_cells = NULL, milestones = NULL,
  milestone_percentages = trajectory$milestone_percentages,
  grouping = NULL, groups = NULL, cell_feature_importances = NULL,
  heatmap_type = c("tiled", "dotted"),
  scale = dynutils::scale_quantile, label_milestones = TRUE)

Arguments

trajectory	The trajectory
expression_source	Source of the feature expression, defaults to `expression`
features_oi	The features of interest, either the number of features or a vector giving the names of the different features
clust	The method to cluster the features, or a hclust object
margin	The margin to add
color_cells	How to color the cells
milestones	Tibble containing the `milestone_id` and a `color` for each milestone
milestone_percentages	The milestone percentages
grouping	The grouping of the cells
groups	Tibble containing information of the cell groups
cell_feature_importances	The importances of every feature in every cell, as returned by [dynfeature::calculate_cell_feature_importance()]
heatmap_type	The type of heatmap, either tiled or dotted
scale	Whether to rescale the expression, can be a function or boolean
label_milestones	How to label the milestones. Can be TRUE (in which case the labels within the trajectory will be used), "all" (in which case both given labels and milestone_ids will be used), a named character vector, or FALSE

Examples

data(example_linear)
plot_heatmap(example_linear)
#> No features of interest provided, selecting the top 20 features automatically
#> Using dynfeature for selecting the top 20 features
#> Loading required namespace: dynfeature
#> root cell or milestone not provided, trying first outgoing milestone_id
#> Using 'M1' as root
#> Coloring by milestone
data(example_bifurcating)
plot_heatmap(example_bifurcating)
#> No features of interest provided, selecting the top 20 features automatically
#> Using dynfeature for selecting the top 20 features
#> root cell or milestone not provided, trying first outgoing milestone_id
#> Using 'M1' as root
#> Coloring by milestone