First commit

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

00-install.R

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+
+# Essentials ----
+
+install.packages("BiocManager")
+BiocManager::install("iSEE")
+install.packages("rsconnect")
+
+# GitHub ----
+
+# For some reason rsconnect::deployApp() doesn't seem to like GitHub
+# install.packages("devtools")
+# devtools::install_github("csoneson/iSEE")

01-subset-allen.R

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+# Due to the memory limit on RStudio Cloud sessions, the full "allen" dataset could not be used for the demo.
+# This script was run on a local machine to load and subset the "allen" dataset.
+# The RDS file containing the subset was then uploaded to a Dropbox account from which it was downloaded from the RStudio Cloud session.
+# Please refer to "02-subset-download.R" for that last step.
+
+library(scRNAseq)
+data("allen")
+
+# Subset assays ----
+assayNames(allen)
+assay(allen, "counts") <- assay(allen, "tophat_counts")
+for (x in setdiff(assayNames(allen), "counts")) {
+  assay(allen, x) <- NULL
+}
+allen
+
+# Subset colData ----
+colnames(colData(allen))
+colData(allen) <- colData(allen)[, c("NREADS", "driver_1_s", "dissection_s", "Core.Type", "passes_qc_checks_s")]
+
+# There is no colData ----
+rowData(allen)
+
+# Drop metadata ----
+metadata(allen) <- list()
+
+# Normalize ----
+library(scater)
+sce <- as(allen, "SingleCellExperiment")
+sce <- normalize(sce)
+
+# Add reduced dimensions ----
+sce <- runPCA(sce, ncomponents=4)
+sce <- runTSNE(sce)
+
+# Subset features ----
+keep <- which(order(rowVars(assay(sce, "logcounts"))) <= 500) # keep 500 most variable
+sce <- sce[keep, ]
+
+# Add rowData ----
+rowData(sce)$ave_count <- rowMeans(counts(sce))
+rowData(sce)$n_cells <- rowSums(counts(sce)>0)
+sce
+
+# save to RDS ----
+saveRDS(sce, "allen.subset.rds")

02-subset-download.R

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+# Due to the memory limit on RStudio Cloud sessions, the full "allen" dataset could not be used for the demo.
+# This script was run from the RStudio Cloud session to download a subset of the data, preprocessed on a local machine.
+# Please refer to "01-subset-allen.R" for the preprocessing.
+
+
+BiocManager::install("BiocFileCache")
+
+library(BiocFileCache)
+bfc <- BiocFileCache()
+
+url <- "https://www.dropbox.com/s/yps03y6ws8rtc1h/allen.subset.rds?dl=1"
+if (identical(nrow(bfcquery(bfc, "AllenSubset")), 0L)) {
+  add5 <- bfcadd(bfc, "AllenSubset", fpath=url)
+}
+rid5 <- names(add5)
+
+file.copy(add5, "allen.subset.rds")

99-deploy.R

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+
+library(rsconnect)
+# rsconnect::setAccountInfo(name='kevinrue', token='xxxx', secret='xxx')
+options(repos = BiocManager::repositories())
+rsconnect::deployApp()

app.R

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+
+library(SingleCellExperiment)
+sce <- readRDS("allen.subset.rds")
+
+library(iSEE)
+library(shiny)
+
+# Preload the tour, so that it opens on startup
+tour <- read.delim(system.file(package = "iSEE", "extdata", "intro_firststeps.txt"), header = TRUE, sep = ";")
+packageVersion("iSEE")
+iSEE(sce, tour = tour)

isee-shiny-contest.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes

rsconnect/shinyapps.io/kevinrue/isee-shiny-contest.dcf

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+name: isee-shiny-contest
+title: iSEE app using a subset of the allen dataset
+username: kevinrue
+account: kevinrue
+server: shinyapps.io
+hostUrl: https://api.shinyapps.io/v1
+appId: 735398
+bundleId: 1894024
+url: https://kevinrue.shinyapps.io/isee-shiny-contest/
+when: 1550950950.2006