Plot PCA Score by Batch

Draw a PCA score plot for samples and color points by batch. PCA is computed on log2-transformed intensities after removing variables with missing values.

Usage

plot_batch_pca(exp, batch_col = "batch")

Arguments

exp

A glyexp::GlycomicSE(), glyexp::GlycoproteomicSE(), or SummarizedExperiment::SummarizedExperiment() object.

batch_col

Column name in sample_info, or a factor/vector with length equal to the number of samples.

Value

A ggplot object of PCA scores.

Examples

library(SummarizedExperiment)

exp <- glyexp::real_experiment
batch <- rep(c("A", "B"), length.out = ncol(exp))
colData(exp)$batch <- batch
plot_batch_pca(exp, batch_col = "batch")