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
)
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
Examples
#> The parameter 'n_neighbors' cannot be bigger than the total number of samples. Setting 'n_neighbors' to 7.
plot_umap(res_annot, "none")