In ipatop/FlyCellAtlas.download.with.annotations: Reads and process loom files from FlyCellAtlas to be compatible with Seurat

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

#devtools::install_github("ipatop/FlyCellAtlas.download.with.annotations")
library(FlyCellAtlas.download.with.annotations)

General

This package is designed to analyze the data from the FlyCellAtlas

Dependencies

This packages depends on the following packages, they should be loaded automatically but just in case if you want you can load them manually

library("assertthat")
library("Seurat")
library("SeuratDisk")
library("grDevices")
library("ggplot2")
library("hdf5r")
library("loomR")
library("scater")
library("patchwork")
library("SeuratObject")
library("dplyr")
library("tidyr")
library("cowplot")

Run example data

#Files are in https://flycellatlas.org
# Here we download the body wall 10X loom and h5ad
download.file(url = "https://cloud.flycellatlas.org/index.php/s/egxzns8NgtCjonB/download",destfile = "./bodywall.loom")
download.file(url = "https://cloud.flycellatlas.org/index.php/s/sZZMSbcNk4SWtHE/download",destfile = "./bodywall.h5ad")

loom_file<-"./bodywall.loom"
h5ad_file<-"./bodywall.h5ad"
## basic example code to create a new Seurat object with annotations from FlyCellAtlas
bodywall_new<-loom_too_Seurat_brandNew(loom_file =loom_file,h5ad_file=h5ad_file)

Now bodywall_new is a Seurat object we can not plot etc

DimPlot(bodywall_new,repel = T,label = T,reduction = "umap", group.by = "annotation")+ NoLegend()

ipatop/FlyCellAtlas.download.with.annotations documentation built on March 26, 2022, 1:46 a.m.