PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.
You can install the released version of PathwayEmbed from GitHub using:
# Install remotes if you haven't already
if (!requireNamespace("remotes", quietly = TRUE)) {
install.packages("remotes")
}
remotes::install_github("RaredonLab/PathwayEmbed")
library(PathwayEmbed)
# Load example data included with the package
data(fake_test_matrix)
data(fake_test_metadata)
# Compute pathway data
mds_results <- ComputeCellData(fake_test_matrix, pathway = "Wnt", distance.method = "manhattan", batch.size = 100)
# Prepare data for plotting
plot_data <- PreparePlotData(fake_test_metadata, mds_results, group = "genotype")
# Plot pathway activation
PlotPathway(to.plot = plot_data, pathway = "Wnt", group = "genotype", color = c("#ae282c", "#2066a8"))
# Calculate percentage and do comparison between two groups (optional)
CalculatePercentage(to.plot = plot_data, group_var = "genotype")