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PathwayEmbed

We are focusing on estimating intracellular signal transduction states vis distance embedding

PathwayEmbed

Build Status License: MIT

PathwayEmbed is an R package for quantifying and visualizing intracellular signaling pathway activation from transcriptomic data, integrating pathway topology and gene expression data.

Installation

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")

Usage 

library(PathwayEmbed)

# Load example data included with the package
data("synthetic_test_object_100")
data("synthetic_test_metadata")

# Check what pathways are availabel in the pre-constructed table
ListPathway() # summary page
ListPathway("Pathway") # what pathways are available
ListPathway("WNT") # what coefficient tables are available

# Load pre-constructed pathway coefficient tables
Wnt_12h   <- LoadPathway("WNT3A_12H_ACTIVATION",  "mouse")

# Input data preprocess 
matrix_12h   <- DataPreProcess(synthetic_test_object_100, Wnt_12h,   Seurat.object = TRUE)

# Determine the global reference (ON and OFF)
pathwaystat_12h   <- PathwayMaxMin(matrix_12h,   Wnt_12h)

# Compute pathway data
score_12h   <- ComputeCellData(matrix_12h,   pathwaystat_12h)

# Prepare data for plotting
plot_data_12h   <- PreparePlotData(synthetic_test_metadata, score_12h,   group = "genotype")

# Plot pathway activation
PlotPathway(plot_data_12h,   "12hr Wnt",    "genotype", c("#ae282c", "#2066a8"))

# Calculate percentage and do comparison between two groups (optional)
 CalculatePercentage(to.plot = plot_data_12h,   group_var = "genotype")