pcvr (version 1.2.0)

pcadf: Function to run a PCA, plot and optionally return the data with PCA coordinates and pca object

Description

Function to run a PCA, plot and optionally return the data with PCA coordinates and pca object

Usage

pcadf(
  df = NULL,
  cols = NULL,
  color = NULL,
  facet = NULL,
  returnData = TRUE,
  ncp = NULL
)

Value

A ggplot or list with a ggplot, a dataframe with the data and PCs, and the factominer PCA object as elements.

Arguments

df

Dataframe to ordinate

cols

columns to reduce dimensions of. Can be specified with names or positions. If this is length of 1 then it is treated as regex pattern to match the column names that should be used.

color

column name(s) used to color points in the pca plot.

facet

Optional column or vector to facet plots on.

returnData

Logical, should data be returned?

ncp

Optional, number of principal components to return attached to dataframe if data is returned. Defaults to all.

Details

If data is returned then it will contain the coordinates from the PCA and will not contain the columns that were reduced.

Examples

dists <- list(
  rlnorm = list(meanlog = log(40), sdlog = 0.5),
  rnorm = list(mean = 60, sd = 10)
)
mv <- mvSim(
  dists = dists, n_samples = 100, counts = 1000,
  min_bin = 1, max_bin = 180, wide = TRUE
)
mv$otherGroup <- sample(c("a", "b"), size = nrow(mv), replace = TRUE)
pcadf(mv, cols = "sim_", returnData = TRUE)
pcadf(mv, cols = 2:181, color = c("group", "otherGroup"), returnData = FALSE)