runMatrixAnalysis: Runs a matrix analysis (clustering, kmeans, pca).

In thebustalab/phylochemistry: Chemical and Sequence Analyses in a Phylogenetic Context

Description

Runs a matrix analysis (clustering, kmeans, pca).

Usage

runMatrixAnalysis(
  data,
  analysis = c("hclust", "pca", "pca-ord", "pca-dim"),
  column_w_names_of_multiple_analytes = NULL,
  column_w_values_for_multiple_analytes = NULL,
  columns_w_values_for_single_analyte = NULL,
  columns_w_additional_analyte_info = NULL,
  columns_w_sample_ID_info = NULL,
  transpose = FALSE,
  unknown_sample_ID_info = NULL,
  scale_variance = TRUE,
  kmeans = c("none", "auto", "elbow", "1", "2", "3", "etc."),
  na_replacement = c("none", "mean", "zero", "drop"),
  output_format = c("wide", "long"),
  ...
)

Arguments

data	The data frame or tibble to analyze
analysis	The type of analysis to run. Can be one of: "hclust" (heirarchical clustering), "pca" (principal components analysis), "pca-ord" (principal components analysis ordination plot), or "pca-dim" (principal components scree plot)
column_w_names_of_multiple_analytes

thebustalab/phylochemistry documentation built on Sept. 3, 2021, 5:06 a.m.