plot_mx_umap {mxnorm}

Visualize UMAP dimension reduction algorithm

Description

Visualize UMAP dimension reduction algorithm

Usage

plot_mx_umap(mx_data, metadata_col = NULL)

Arguments

mx_data

mx_dataset object that been used with run_reduce_umap() to compute the UMAP dimensions for the dataset. Note that the table attribute must be set when running run_reduce_umap().

metadata_col

column denoted in the run_reduce_umap() to change the scale_color attribute of the ggplot (default=NULL)

Value

ggplot2 object with density plot

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"))
plot_mx_umap(mx_data)