runGiottoHarmony#
Last Updated: Sep 07, 2023
Description#
run UMAP
Usage#
runGiottoHarmony(
gobject,
spat_unit = NULL,
feat_type = NULL,
vars_use = "list_ID",
do_pca = FALSE,
expression_values = c("normalized", "scaled", "custom"),
reduction = "cells",
dim_reduction_to_use = "pca",
dim_reduction_name = NULL,
dimensions_to_use = 1:10,
name = NULL,
feats_to_use = NULL,
toplevel_params = 2,
return_gobject = TRUE,
verbose = NULL,
...
)
Arguments#
|
giotto object |
|
spatial unit |
|
feature type |
|
If meta_data is dataframe, this defines which variable(s) to remove (character vector). |
|
Whether to perform PCA on input matrix. |
|
expression values to use |
|
reduction on cells or features |
|
use another dimension reduction set as input |
|
name of dimension reduction set to use |
|
number of dimensions to use as input |
|
arbitrary name for Harmony run |
|
if dim_reduction_to_use = NULL, which feats to use |
|
parameters to extract |
|
boolean: return giotto object (default = TRUE) |
|
be verbose |
|
additional |
Details#
This is a simple wrapper for the HarmonyMatrix function in the Harmony package doi:10.1038/s41592-019-0619-0.
Value#
giotto object with updated Harmony dimension recuction