plot_SVD_kmeans: Plot the first two PCs from logistic SVD for molecular...

In blind-contours/ChemLogic: Pipeline of methods that take in chemical fingerprint and molecular physical information and creates interpretable rules based on this information which leads to nuclear receptor binding

Description

This function takes in a binary matrix, assuming that the variable names include the fingerprint name such as "Pubchem"

Usage

plot_SVD_kmeans(
  receptor_type,
  log_SVD_results,
  binary_data,
  k = 4,
  endo_ligand = FALSE,
  endo_ligand_id,
  additional_label = TRUE,
  outcome_label = "ASSAY_OUTCOME"
)

Arguments

receptor_type	type of receptor for labeling plots
log_SVD_results	Results from the SVD to get data from for plotting
k	number of groups from kmeans from after viewing elbow plot or other methods of determining groups

Value

Plot of SVD results colored by kmeans groups

blind-contours/ChemLogic documentation built on July 7, 2020, 5:34 a.m.