nanostringPCA {NanoTube}R Documentation

Plot PCA

Description

Conduct principal components analysis and plot the results, using either ggplot2 or plotly.

Usage

nanostringPCA(
  ns,
  pc1 = 1,
  pc2 = 2,
  interactive.plot = FALSE,
  exclude.zeros = TRUE
)

Arguments

ns

Processed NanoString data

pc1

Principal component to plot on x-axis (default 1)

pc2

Principal component to plot on y-axis (default 2)

interactive.plot

Plot using plotly? Default FALSE (in which case ggplot2 is used)

exclude.zeros

Exclude genes that are not detected in all samples (default TRUE)

Value

A list containing:

pca

The PCA object

plt

The PCA plot

Examples

example_data <- system.file("extdata", "GSE117751_RAW", package = "NanoTube")
sample_data <- system.file("extdata", "GSE117751_sample_data.csv", 
                           package = "NanoTube")

# Process and normalize data first
dat <- processNanostringData(example_data, 
                             sampleTab = sample_data, 
                             groupCol = "Sample_Diagnosis",
                             normalization = "nSolver", 
                             bgType = "t.test", bgPVal = 0.01)
                               
# Interactive PCA using plotly                             
nanostringPCA(dat, interactive.plot = TRUE)$plt

# Static plot using ggplot2, for the 3rd and 4th PC's.
nanostringPCA(dat, pc1 = 3, pc2 = 4, interactive.plot = FALSE)$plt

[Package NanoTube version 1.0.0 Index]