HCAExplorer.R
In HCAExplorer: Browse the Human Cell Atlas data portal

## ----init, results='hide', echo=FALSE, warning=FALSE, message=FALSE-----------
library(knitr)
opts_chunk$set(warning=FALSE, message=FALSE)
BiocStyle::markdown()

## ----install_bioc, eval=FALSE-------------------------------------------------
#  if (!require("BiocManager"))
#      install.packages("BiocManager")
#  BiocManager::install('HCAExplorer')

## ----libraries, message=FALSE-------------------------------------------------
library(HCAExplorer)

## ----createHCA----------------------------------------------------------------
hca <- HCAExplorer(url = 'https://service.explore.data.humancellatlas.org', per_page = 15)
hca

## ----results------------------------------------------------------------------
results(hca)

## ----select-------------------------------------------------------------------
hca <- hca %>% select('projects.projectTitle', 'samples.organ')
hca

## ----resetSelect--------------------------------------------------------------
hca <- resetSelect(hca)
hca

## ----activate-----------------------------------------------------------------
## The HCAExplorer object is activated here by 'samples'
hca <- hca %>% activate('samples')
hca

## Revert back to showing projects with 'projects'
hca <- hca %>% activate('projects')
hca

## ----nextResults--------------------------------------------------------------
hca <- nextResults(hca)
hca

## ----fields-------------------------------------------------------------------
hca <- HCAExplorer()
fields(hca)

## ----valuess------------------------------------------------------------------
values(hca, 'organ')

## ----firstFilter--------------------------------------------------------------
hca2 <- hca %>% filter(organ == c('blood', 'brain'))
hca <- hca %>% filter(organ %in% c('blood', 'brain'))
hca

## ----second_values------------------------------------------------------------
values(hca, 'disease')

## ----multiFilter--------------------------------------------------------------
hca <- hca %>% filter(disease == 'normal')
hca <- undoQuery(hca, n = 2L)

hca <- hca %>% filter(organ %in% c('Brain', 'brain'), disease == 'normal')
hca <- resetQuery(hca)

hca <- hca %>% filter(organ %in% c('Brain', 'brain') & disease == 'normal')
hca

## ----subsetting---------------------------------------------------------------
hca <- hca[1:2,]
hca

## ----getManifestFileFormats---------------------------------------------------
formats <- getManifestFileFormats(hca)
formats

## ----getManifest--------------------------------------------------------------
manifest <- getManifest(hca, fileFormat = formats[1])
manifest

## ----checkExpressionMatricesAvailability--------------------------------------
hca <- HCAExplorer()
checkExpressionMatricesAvailability(hca, format = "loom")

## ----downloadExpressionMatrix, eval = FALSE-----------------------------------
#  ## Create HCAExplorer object
#  hca <- HCAExplorer()
#  
#  ## Obtain the fifth project by subsetting
#  hca <- hca[5]
#  
#  ## Download project's expression matrix file as a LoomExperiment object
#  le <- downloadExpressionMatrices(hca, format = "loom", useBiocFileCache = FALSE)
#  le

## ----sessionInfo--------------------------------------------------------------
sessionInfo()