nicePCA: 'nicePCA'

In saezlab/ocean: metabolic enzyme enrichment analysis

nicePCA

Description

This function generate a 3*3 arrangeGrob plot object (that can be subsequently diplayed or saved). Each cell of the 3*3 plot grid correspond to a specific representation of the result of a principal component analysis performed on a measurment dataframe. The first input is a n*m data.frame, where n is the number of measured omic features (genes, proteins, metabolites...) and m is the number of samples. The second input is a basic n*2 target dataframe (such as generated by the generateTarget function), where n is the number of samples.

Usage

nicePCA(
  df,
  targets,
  components = c(1, 2, 3),
  centering = T,
  scaling = F,
  pointSize = 4,
  no_label = FALSE
)

Arguments

df	the measurment n*m dataframe (n is number of omic features, m is number of samples) where columns are ordered by conditions.
targets	A n*2 dataframe, where n is the number of samples. First column correspond to samples, second column correspond to conditions.
components	a vector of three integers, corresponding to the components to be plotted
centering	a boolean parameter to indicate wether samples should be mean centered
scaling	a boolean parameter to indicate wether samples should be scaled (x/variance)
pointSize	an integer parameter to indicate the desired point size for the components scatter plots.

Value

an 3*3 arrangeGrob object containing various graphical representation of the result of a PCA.

saezlab/ocean documentation built on Nov. 12, 2024, 5 a.m.