dimension_reduction-HierarchicalPartition-method {cola} | R Documentation |
Visualize columns after dimension reduction
## S4 method for signature 'HierarchicalPartition' dimension_reduction(object, depth = max_depth(object), parent_node, top_n = NULL, method = c("PCA", "MDS", "t-SNE", "UMAP"), silhouette_cutoff = 0.5, scale_rows = TRUE)
object |
A |
depth |
Depth of the hierarchy. |
top_n |
Top n rows to use. By default it uses all rows in the original matrix. |
parent_node |
Parent node. If it is set, the function call is identical to |
method |
Which method to reduce the dimension of the data. |
silhouette_cutoff |
Cutoff of silhouette score. Data points with values less than it will be mapped to small points. |
scale_rows |
Whether perform scaling on matrix rows. |
The class IDs are extract at depth
.
No value is returned.
Zuguang Gu <z.gu@dkfz.de>
data(cola_rh) dimension_reduction(cola_rh) dimension_reduction(cola_rh, parent_node = "00")