nanostringPCA {NanoTube} | R Documentation |
Conduct principal components analysis and plot the results, using either ggplot2 or plotly.
nanostringPCA( ns, pc1 = 1, pc2 = 2, interactive.plot = FALSE, exclude.zeros = TRUE )
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) |
A list containing:
pca |
The PCA object |
plt |
The PCA plot |
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