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