plot_heatmap.Rd
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)
trajectory | The trajectory |
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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 |
#> 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#> 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