diff --git a/demo/GlobalPatterns.RDS b/demo/GlobalPatterns.RDS new file mode 100644 index 0000000000000000000000000000000000000000..8b56d995b3742265e9fc5b58a8b2219b89b37166 Binary files /dev/null and b/demo/GlobalPatterns.RDS differ diff --git a/demo/demo.RData b/demo/demo.RData deleted file mode 100644 index 950b79ed96c2747ca04c97e28a48af224ed1417b..0000000000000000000000000000000000000000 Binary files a/demo/demo.RData and /dev/null differ diff --git a/demo/food.RDS b/demo/food.RDS new file mode 100644 index 0000000000000000000000000000000000000000..73f0cb2f4fac6a09958216b1d0c48fb5d6e341df Binary files /dev/null and b/demo/food.RDS differ diff --git a/demo/make-demo.R b/demo/make-demo.R index c5c6da86ecc0272d36152c1fcfc77e29a7b9ddf8..2432f5a9fe4c5e027f4a505cc7f143577456bb33 100644 --- a/demo/make-demo.R +++ b/demo/make-demo.R @@ -4,55 +4,57 @@ data("GlobalPatterns") food <- import_biom( - BIOMfilename = "chaillou.biom", - treefilename = "chaillou.nwk", + BIOMfilename = "demo/chaillou.biom", + treefilename = "demo/chaillou.nwk", parseFunction = parse_taxonomy_greengenes ) sample_data(food) <- - read.table("chaillou.tsv", + read.table("demo/chaillou.tsv", header = TRUE, row.names = 1, sep = "\t") -kinetic <- - import_biom(BIOMfilename = "mach.biom", treefilename = "mach.nwk") -sample_data(kinetic) <- - read.table("mach.tsv", - header = TRUE, - row.names = 1, - sep = "\t") -colnames(tax_table(kinetic)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus") -tax_table(kinetic)[grep("unknown ", tax_table(kinetic))] <- NA - -ravel <- - import_biom(BIOMfilename = "ravel.biom") -sample_data(ravel) <- - read.table("ravel.tsv", - header = TRUE, - row.names = 1, - sep = "\t") -colnames(tax_table(ravel)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") -tax_table(ravel)[grep("unknown ", tax_table(ravel))] <- NA - -soil <- - import_biom(BIOMfilename = "morton.biom", treefilename = "morton.tree") -sample_data(soil) <- - read.table("morton.csv", - header = TRUE, - row.names = 1, - sep = "\t") -colnames(tax_table(soil)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") -tax_table(soil)[grep("unknown ", tax_table(soil))] <- NA - -biorare <- - import_biom(BIOMfilename = "biorare.biom", treefilename = "biorare.nwk") -sample_data(biorare) <- - read.table("biorare.tsv", header = TRUE, row.names = 1) -colnames(tax_table(biorare)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") -tax_table(biorare)[grep("unknown ", tax_table(biorare))] <- NA - +# kinetic <- +# import_biom(BIOMfilename = "mach.biom", treefilename = "mach.nwk") +# sample_data(kinetic) <- +# read.table("mach.tsv", +# header = TRUE, +# row.names = 1, +# sep = "\t") +# colnames(tax_table(kinetic)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus") +# tax_table(kinetic)[grep("unknown ", tax_table(kinetic))] <- NA +# +# ravel <- +# import_biom(BIOMfilename = "ravel.biom") +# sample_data(ravel) <- +# read.table("ravel.tsv", +# header = TRUE, +# row.names = 1, +# sep = "\t") +# colnames(tax_table(ravel)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") +# tax_table(ravel)[grep("unknown ", tax_table(ravel))] <- NA +# +# soil <- +# import_biom(BIOMfilename = "morton.biom", treefilename = "morton.tree") +# sample_data(soil) <- +# read.table("morton.csv", +# header = TRUE, +# row.names = 1, +# sep = "\t") +# colnames(tax_table(soil)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") +# tax_table(soil)[grep("unknown ", tax_table(soil))] <- NA +# +# biorare <- +# import_biom(BIOMfilename = "biorare.biom", treefilename = "biorare.nwk") +# sample_data(biorare) <- +# read.table("biorare.tsv", header = TRUE, row.names = 1) +# colnames(tax_table(biorare)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") +# tax_table(biorare)[grep("unknown ", tax_table(biorare))] <- NA +# # cellulose <- import_biom(BIOMfilename = "cellulose.biom") # sample_data(cellulose) <- read.table("cellulose.tsv", header = TRUE, row.names = 1) # save(GlobalPatterns, food, kinetic, soil, ravel, biorare, file = "demo.RData") -save(food, file = "demo.RData") + +saveRDS(food, file = "demo/food.RDS") +saveRDS(GlobalPatterns, file = "demo/GlobalPatterns.RDS") \ No newline at end of file diff --git a/panels/dataInput.R b/panels/dataInput.R index 30eb46d856f1fb938aded01ddf99401019b4ce47..aee7f1d1bbcf363bb8cbba6a79601bfd7a7c8db8 100644 --- a/panels/dataInput.R +++ b/panels/dataInput.R @@ -127,13 +127,7 @@ observeEvent(input$okData, { "demo" = { message <- as.character(input$demo) - ne <- new.env() - if (!is.null(input$demo)) - { - data(GlobalPatterns) - load("demo/demo.RData", envir = ne) - get(input$demo) - } + readRDS(paste0("demo/", input$demo,".RDS")) }, "input" = {