run_reduce_umap {mxnorm}

Run UMAP dimension reduction algorithm on an mx_dataset object.

Description

Run UMAP dimension reduction algorithm on an mx_dataset object.

Usage

run_reduce_umap(
  mx_data,
  table,
  marker_list,
  downsample_pct = 1,
  metadata_cols = NULL
)

Arguments

mx_data

mx_dataset object used to compute UMAP dimensions

table

dataset in mx_data used to compute metrics. Options include: c("raw","normalized","both"), e.g. a y-axis parameter.

marker_list

list of markers in the mx_dataset object to use for UMAP algorithm

downsample_pct

double, optional percentage (0, 1] of sample rows to include when running UMAP algorithm. (default=1)

metadata_cols

other identifiers of the input data (default=NULL). This must be a vector of column name(s) in the mx_dataset object

Value

mx_dataset object with analysis results of UMAP dimension results in umap_data table

Examples

mx_data = mx_dataset(mxnorm::mx_sample, "slide_id", "image_id",
  c("marker1_vals","marker2_vals","marker3_vals"),
  c("metadata1_vals"))
mx_data = mx_normalize(mx_data, transform="log10",method="None")
mx_data = run_reduce_umap(mx_data, table="normalized",
c("marker1_vals","marker2_vals","marker3_vals"))