Chapter 3 Quick-start

3.1 Installation

3.1.1 Installation from GitHub

This requires the devtools package to be pre-installed first. The HematoMap also required for pre-installation of the Seurat package (https://satijalab.org/seurat/).

# If Seurat is not already installed, you need to install Seurat first
install.packages("Seurat") 

# If devtools is not already installed, you need to install devtools first
install.packages("devtools")

To install HematoMap

# Installation of HematoMap
devtools::install_github("NRCTM-bioinfo/HematoMap")

# library HematoMap
library(HematoMap)

The source code of HematoMap on GitHub can be accessed at https://github.com/NRCTM-bioinfo/HematoMap.

In this chapter, we will describe the main functionalities and a quick-start code template for the workflow of HematoMap. The necessary data for this chapter is already included in the HematoMap package. By reading this chapter, you will learn:

1. Gain an overview of the workflow and the built-in database of HematoMap.
1. A quick-start code about how to use HematoMap.

And for the detailed version and advanced application of HematoMap, please read Chapter 4 and Chapter 5.

3.2 Load package

# library the Seurat and HematoMap packages
library(Seurat)
library(pbmcapply)
library(HematoMap)

3.3 Show normal BMMCs

# Show circle plot of normal BMMC
plotCircleTree(group.subc = "reference", 
               color.mapping = "cell.type", 
               title = "Normal BMMCs")

# Show cluster-tree plot of normal BMMC
plotClusterTree(group.subc = "reference",
                color.mapping = "cell.type",
                title = "Normal BMMCs",
                point.size = 20, 
                label.cell = TRUE)

3.4 Quick-start code

# For scRNA-seq analysis
# the `scrna` is a seurat object
hmap <- HematoMap::CreateSubclusterObject(scrna)

# For bulk RNA-seq analysis
# the `bulk` is a expression matrix of bulk RNA-seq
hmap.bulk <- computeLassoScore(bulk)