---
title: "WeberDivechaLCdata package"
author: 
  - name: Lukas M. Weber
    affiliation: "Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA"
  - name: Heena R. Divecha
    affiliation: "Lieber Institute for Brain Development, Baltimore, MD, USA"
package: WeberDivechaLCdata
output: 
  BiocStyle::html_document
vignette: >
  %\VignetteIndexEntry{WeberDivechaLCdata package}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```


# Introduction

This package contains data from our paper on the gene expression landscape of the human locus coeruleus (LC).

The dataset consists of spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from the LC in postmortem human brain samples. Data were generated with the 10x Genomics Visium SRT and 10x Genomics Chromium snRNA-seq platforms.

The data are provided as `SpatialExperiment` and `SingleCellExperiment` R/Bioconductor objects in this package, and in online web apps (`Shiny` and `iSEE`) for interactive exploration (see links in paper).

A preprint of the paper is available from [bioRxiv](https://www.biorxiv.org/content/10.1101/2022.10.28.514241v1).


## Installation

The package can be installed from Bioconductor ([WeberDivechaLCdata](https://bioconductor.org/packages/WeberDivechaLCdata)) as follows:

```{r, eval=FALSE}
install.packages("BiocManager")
BiocManager::install("WeberDivechaLCdata")
```


## Contents

The package contains the following objects:

- `WeberDivechaLCdata_Visium`: SRT (Visium) dataset
- `WeberDivechaLCdata_singleNucleus`: snRNA-seq dataset


# Loading the data

The data objects can be loaded using the dataset names as follows:

```{r, message=FALSE}
library(SpatialExperiment)
library(SingleCellExperiment)
library(WeberDivechaLCdata)
```

```{r, message=FALSE}
# Load objects using dataset names
spe <- WeberDivechaLCdata_Visium()
sce <- WeberDivechaLCdata_singleNucleus()
```


Alternatively, the data objects can be loaded by accessing the ExperimentHub 
IDs:

```{r, message=FALSE}
library(ExperimentHub)
```

```{r, message=FALSE}
# create ExperimentHub instance
eh <- ExperimentHub()

# query datasets
my_files <- query(eh, "WeberDivechaLCdata")
my_files

# metadata
md <- as.data.frame(mcols(my_files))
```

```{r, message=FALSE}
# load data using ExperimentHub query
spe <- my_files[[1]]
sce <- my_files[[2]]
```

```{r, message=FALSE}
# load data using ExperimentHub IDs
# spe <- myfiles[["EHXXXX"]]
# sce <- myfiles[["EHYYYY"]]
```


## Show data

Check that the data have been loaded:

```{r, message=FALSE}
# Visium data (SpatialExperiment format)
spe

# dimensions
dim(spe)
# assays
assayNames(spe)
# row data
rowData(spe)
# column data
colData(spe)
# spatial coordinates
head(spatialCoords(spe))
# image data
imgData(spe)
```


```{r, message=FALSE}
# snRNA-seq data (SingleCellExperiment format)
sce

# dimensions
dim(sce)
# assays
assayNames(sce)
# row data
rowData(sce)
# column data
colData(sce)
```


# Session information

```{r}
sessionInfo()
```