Plots samples on a UMAP scatterplot. Samples can be colored by the levels of mutational signatures or by a annotation variable.
plot_umap( result, color_by = c("signatures", "annotation", "cluster", "none"), proportional = TRUE, annotation = NULL, point_size = 0.7, same_scale = TRUE, add_annotation_labels = FALSE, annotation_label_size = 3, annotation_text_box = TRUE, plotly = FALSE, clust = NULL, legend = TRUE, strip_axes = FALSE )
result | A |
---|---|
color_by | One of |
proportional | If |
annotation | Sample annotation used to color the points. One used
when |
point_size | Scatter plot point size. Default |
same_scale | If |
add_annotation_labels | If |
annotation_label_size | Size of annotation labels. Only used if
codecolor_by = "annotation" and |
annotation_text_box | Place a white box around the annotation labels
to improve readability. Only used if codecolor_by = "annotation" and
|
plotly | If |
clust | Add cluster labels as annotation |
legend | Plot legend |
strip_axes | Remove axes labels for cleaner looking plots |
Generates a ggplot or plotly object
See create_umap to generate a UMAP in a musica result.
data(res_annot) create_umap(res_annot, "Tumor_Subtypes") #> The parameter 'n_neighbors' cannot be bigger than the total number of samples. Setting 'n_neighbors' to 7. plot_umap(res_annot, "none")