plot_pca_v1: PCA Plot

In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

Description

A convenience function for plotting PCA scatter plot for samples in ExpressionSet/MSnSet object.

Usage

plot_pca_v1(
  eset,
  phenotype = NULL,
  show.ellispe = TRUE,
  show.NA = TRUE,
  legend.title.width = 20
)

plot_pca_v2(eset, phenotype = NULL, names = FALSE)

plot_pca_v3(
  eset,
  phenotype = NULL,
  label = NULL,
  point_size = 5,
  show.ellispe = TRUE,
  show.NA = TRUE,
  legend.title.width = 20,
  ...
)

plot_pca_v4(
  eset,
  phenotype = NULL,
  label = NULL,
  point_size = 5,
  show.ellispe = TRUE,
  show.NA = TRUE,
  legend.title.width = 20,
  pc.index = c(1, 2),
  ...
)

Arguments

eset	eset (or most likely eset subclass) object
phenotype	character one of the colnames(pData(eset))
show.NA	logical Should the datapoints for which phenotype is unknown be shown? Default is TRUE
legend.title.width	integer Wrapping up too long legend titles. Passed to stringr::str_wrap as width argument. Default is 20.
show.ellipse	logical determining to plot 95% CI based on Hotelling's T-test or not.

Value

plot

Functions

• plot_pca_v2: Alternative PCA

• plot_pca_v3: Alternative PCA

• plot_pca_v4: Alternative PCA with option to select pair of principal components

Examples

data(srm_msnset)
plot_pca_v1(msnset, phenotype = "subject.type", show.ellispe = F)
plot_pca_v1(msnset, phenotype = "subject.type", show.ellispe = T)
plot_pca_v1(msnset)
data(srm_msnset)
plot_pca_v2(msnset, phenotype = "subject.type")
plot_pca_v2(msnset)
data(srm_msnset)
plot_pca_v3(msnset, phenotype = "subject.type")
plot_pca_v3(msnset, phenotype = "subject.type", label = "sample.id")
plot_pca_v3(msnset)
data(srm_msnset)
plot_pca_v4(msnset, phenotype = "subject.type", pc.index=c(1,3))
plot_pca_v4(msnset, phenotype = "subject.type", label = "sample.id", pc.index=c(1,3))
plot_pca_v4(msnset, pc.index=c(1,3))

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.