plot_umap {musicatk} | R Documentation

## Plot a UMAP from a musica result

### Description

Plots samples on a UMAP scatterplot. Samples can be colored by the levels of mutational signatures or by a annotation variable.

### Usage

    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
    )

### Arguments

`result` | A `musica_result` object generated by a mutational discovery or prediction tool.
`color_by` | One of `"signatures"`, `"annotation"`, or `"none"`. If `"signatures"`, then one UMAP scatterplot will be generated for each signature and points will be colored by the level of that signature in each sample. If `annotation`, a single UMAP will be generated colored by the annotation selected using the parameter `annotation`. If `"none"`, a single UMAP scatterplot will be generated with no coloring. Default `"signature"`.
`proportional` | If `TRUE`, then the exposures will be normalized to between 0 and 1 by dividing by the total number of counts for each sample. Default `TRUE`.
`annotation` | Sample annotation used to color the points. One used when `color_by = "annotation"`. Default `NULL`.
`point_size` | Scatter plot point size. Default `0.7`.
`same_scale` | If `TRUE`, then all points will share the same color scale in each signature subplot. If `FALSE`, then each signature subplot will be colored by a different scale with different maximum values. Only used when `color_by = "signature"`. Setting to `FALSE` is most useful when the maximum value of various signatures are vastly different from one another. Default `TRUE`.
`add_annotation_labels` | If `TRUE`, labels for each group in the `annotation` variable will be displayed. Only used if codecolor_by = "annotation". This not recommended if the annotation is a continuous variable. The label is plotting using the centriod of each group within the `annotation` variable. Default `FALSE`.
`annotation_label_size` | Size of annotation labels. Only used if codecolor_by = "annotation" and `add_annotation_labels = TRUE`. Default `3`.
`annotation_text_box` | Place a white box around the annotation labels to improve readability. Only used if codecolor_by = "annotation" and `add_annotation_labels = TRUE`. Default `TRUE`.
`plotly` | If `TRUE`, the the plot will be made interactive using `plotly`. Not used if `color_by = "signature"` and `same_scale = FALSE`. Default `FALSE`.
`clust` | Add cluster labels as annotation
`legend` | Plot legend
`strip_axes` | Remove axes labels for cleaner looking plots

### Value

Generates a ggplot or plotly object

### See Also

See create_umap to generate a UMAP in a musica result.

### Examples

    data(res_annot)
    create_umap(res_annot, "Tumor_Subtypes")
    plot_umap(res_annot, "none")

[Package musicatk version 1.2.0 Index]