romicsUmap: romicsUmap()

In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines

romicsUmap()

Description

Calculate the umap of the data layer of the romics_object using the package umap. This function require the data to be full in the layer data to be run. Plots the samples on the PCA sample plot, the percentage of explained variance, or both on demand using ggplots2. The colors used for the plotting will correspond to the main_factor of the romics_object. The axis to be plotted can be chosen. The PCA results are calculated using the function romicsPCA (see the documentation of this function for more details).

Usage

romicsUmap(
  romics_object,
  umap_config = umap.defaults,
  method = c("naive", "umap-learn"),
  lock_seed = TRUE,
  seed = 42
)

Arguments

romics_object	has to be a log transformed romics_object created using romicsCreateObject() and transformed using the function log2transform() or log10transform()
umap_config	object of class umap.config (see umap() function documentation)
method	character, implementation. Available methods are 'naive' (an implementation written in pure R) and 'umap-learn' (requires python package 'umap-learn')
lock_seed	has to be TRUE or FALSE to indicate if the seed is locked to enable reproducing plotting
seed	numeric value indicating what seed to use when random seed are used
...	Arguments passed to umap function.

Details

This function will

Value

Returns a umap result

Author(s)

Geremy Clair

PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.