v0.99.23 Added a rooted tree to "GlobalPatterns" dataset

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: phyloseq
-Version: 0.99.22
+Version: 0.99.23
 Date: 2012-02-21
 Title: Handling and analysis of high-throughput
     phylogenetic sequence data.

R/.Rhistory

@@ -1,247 +1,3 @@
-	if( substr(RDA_or_CCA, 1, 1) %in% c("R", "r") ){#
-		mod <- rda.phyloseq(X)		#
-	} else if( substr(RDA_or_CCA, 1, 1) %in% c("C", "c") ){#
-		mod <- cca.phyloseq(X)		#
-	} else {#
-		cat("You did not properly specify the desired ordination method\n")#
-		cat("Please see documentation.\n")		#
-		return()#
-	}
-mod
-	ord_vars <- all.vars(X)[-1]
-ord_vars
-	# default is to use the R.H.S. elements of X as color and shape#
-	plot_ordination_phyloseq(mod,#
-		object = object, #
-		site_shape_category = ord_vars[1],#
-		site_color_category = ord_vars[2]#
-	)
-ex1~
-ex1~laskdjflask
-ex1~.
- X <- ex1~.
-	ord_vars <- all.vars(X)[-1]
-	ord_vars
-plot_ordination_phyloseq(mod, object)
-	list(mod=mod, object=object)
-X <- ex1~Diet
-all.vars(X)[-1]
-	popcall
-X <- ex1~Diet #
-RDA_or_CCA="cca"#
-object=get(all.vars(X)[1])#
-#
-	if( substr(RDA_or_CCA, 1, 1) %in% c("R", "r") ){#
-		mod <- rda.phyloseq(X)		#
-	} else if( substr(RDA_or_CCA, 1, 1) %in% c("C", "c") ){#
-		mod <- cca.phyloseq(X)		#
-	} else {#
-		cat("You did not properly specify the desired ordination method\n")#
-		cat("Please see documentation.\n")		#
-		return()#
-	}#
-#
-	# X <- ex1~.#
-	ord_vars <- all.vars(X)[-1]#
-#
-	# Initialize call list for plot_ordination_phyloseq#
-	popcallList <- list(mod=mod, object=object)#
-#
-	if( ord_vars[1] != "."){#
-		popcallList <- c(popcallList, list(site_color_category = ord_vars[1]))#
-	} #
-	if( length(ord_vars) > 1){#
-		popcallList <- c(popcallList, list(site_shape_category = ord_vars[2]))#
-	}#
-	#
-	popcallList
-X <- ex1~Diet + Sex
-	# X <- ex1~.#
-	ord_vars <- all.vars(X)[-1]#
-#
-	# Initialize call list for plot_ordination_phyloseq#
-	popcallList <- list(mod=mod, object=object)#
-#
-	if( ord_vars[1] != "."){#
-		popcallList <- c(popcallList, list(site_color_category = ord_vars[1]))#
-	} #
-	if( length(ord_vars) > 1){#
-		popcallList <- c(popcallList, list(site_shape_category = ord_vars[2]))#
-	}#
-	#
-	popcallList
-X <- ex1~Diet + Sex#
-RDA_or_CCA="cca"#
-object=get(all.vars(X)[1])#
-#
-	if( substr(RDA_or_CCA, 1, 1) %in% c("R", "r") ){#
-		mod <- rda.phyloseq(X)		#
-	} else if( substr(RDA_or_CCA, 1, 1) %in% c("C", "c") ){#
-		mod <- cca.phyloseq(X)		#
-	} else {#
-		cat("You did not properly specify the desired ordination method\n")#
-		cat("Please see documentation.\n")		#
-		return()#
-	}#
-#
-	# X <- ex1~.#
-	ord_vars <- all.vars(X)[-1]#
-#
-	# Initialize call list for plot_ordination_phyloseq#
-	popcallList <- list(mod=mod, object=object)#
-#
-	if( ord_vars[1] != "."){#
-		popcallList <- c(popcallList, list(site_color_category = ord_vars[1]))#
-	} #
-	if( length(ord_vars) > 1){#
-		popcallList <- c(popcallList, list(site_shape_category = ord_vars[2]))#
-	}#
-	#
-	do.call("plot_ordination_phyloseq", popcallList)
-X <- ex1~Diet + Gender#
-RDA_or_CCA="cca"#
-object=get(all.vars(X)[1])#
-#
-	if( substr(RDA_or_CCA, 1, 1) %in% c("R", "r") ){#
-		mod <- rda.phyloseq(X)		#
-	} else if( substr(RDA_or_CCA, 1, 1) %in% c("C", "c") ){#
-		mod <- cca.phyloseq(X)		#
-	} else {#
-		cat("You did not properly specify the desired ordination method\n")#
-		cat("Please see documentation.\n")		#
-		return()#
-	}#
-#
-	# X <- ex1~.#
-	ord_vars <- all.vars(X)[-1]#
-#
-	# Initialize call list for plot_ordination_phyloseq#
-	popcallList <- list(mod=mod, object=object)#
-#
-	if( ord_vars[1] != "."){#
-		popcallList <- c(popcallList, list(site_color_category = ord_vars[1]))#
-	} #
-	if( length(ord_vars) > 1){#
-		popcallList <- c(popcallList, list(site_shape_category = ord_vars[2]))#
-	}#
-	#
-	do.call("plot_ordination_phyloseq", popcallList)
-X <- ex1 ~ Diet#
-RDA_or_CCA="cca"#
-object=get(all.vars(X)[1])#
-#
-	if( substr(RDA_or_CCA, 1, 1) %in% c("R", "r") ){#
-		mod <- rda.phyloseq(X)		#
-	} else if( substr(RDA_or_CCA, 1, 1) %in% c("C", "c") ){#
-		mod <- cca.phyloseq(X)		#
-	} else {#
-		cat("You did not properly specify the desired ordination method\n")#
-		cat("Please see documentation.\n")		#
-		return()#
-	}#
-#
-	# X <- ex1~.#
-	ord_vars <- all.vars(X)[-1]#
-#
-	# Initialize call list for plot_ordination_phyloseq#
-	popcallList <- list(mod=mod, object=object)#
-#
-	if( ord_vars[1] != "."){#
-		popcallList <- c(popcallList, list(site_color_category = ord_vars[1]))#
-	} #
-	if( length(ord_vars) > 1){#
-		popcallList <- c(popcallList, list(site_shape_category = ord_vars[2]))#
-	}#
-	#
-	do.call("plot_ordination_phyloseq", popcallList)
-X <- ex1 ~ .#
-RDA_or_CCA="cca"#
-object=get(all.vars(X)[1])#
-#
-	if( substr(RDA_or_CCA, 1, 1) %in% c("R", "r") ){#
-		mod <- rda.phyloseq(X)		#
-	} else if( substr(RDA_or_CCA, 1, 1) %in% c("C", "c") ){#
-		mod <- cca.phyloseq(X)		#
-	} else {#
-		cat("You did not properly specify the desired ordination method\n")#
-		cat("Please see documentation.\n")		#
-		return()#
-	}#
-#
-	# X <- ex1~.#
-	ord_vars <- all.vars(X)[-1]#
-#
-	# Initialize call list for plot_ordination_phyloseq#
-	popcallList <- list(mod=mod, object=object)#
-#
-	if( ord_vars[1] != "."){#
-		popcallList <- c(popcallList, list(site_color_category = ord_vars[1]))#
-	} #
-	if( length(ord_vars) > 1){#
-		popcallList <- c(popcallList, list(site_shape_category = ord_vars[2]))#
-	}#
-	#
-	do.call("plot_ordination_phyloseq", popcallList)
-?warning
-class(ex1~.)
-?formula
-library("phyloseq")
-library(phyloseq)
-?ex2
-MHsangerFN <- "~/Dropbox/R/enterotype_example/phylo_tables/MetaHIT_41SangerSamples.genus.txt"#
-MHillumiFN <- "~/Dropbox/R/enterotype_example/phylo_tables/MetaHIT_85IlluminaSamples.genus.txt"#
-TpyroseqFN <- "~/Dropbox/R/enterotype_example/phylo_tables/Turnbaugh_154Pyroseq16S.genus.txt"#
-#
-MHsanger <- read.table(MHsangerFN, TRUE, "\t")#
-MHillumi <- read.table(MHillumiFN, TRUE, "\t")#
-Tpyroseq <- read.table(TpyroseqFN, TRUE, "\t")
-Tpyroseq
-ETaltfile <- "~/Dropbox/R/enterotype_example/ETclassAltLines.txt"
-ETalt <- readLines(ETaltfile)
-ETaltfile <- "~/Dropbox/R/enterotype_example/ETclassAltLines.txt"
-ETalt <- readLines(ETaltfile)
-ETalt
-seq(1, length(ETalt), 2)
-ETalt[seq(1, length(ETalt), 2)]
-ETvalues      <- ETalt[seq(2, length(ETalt), 2)]
-ETvalues
-cbind(samples=ETsampleNames, enterotype=ETvalues)
-ETsampleNames <- ETalt[seq(1, length(ETalt), 2)]
-cbind(samples=ETsampleNames, enterotype=ETvalues)
-ETaltfile <- "~/Dropbox/R/enterotype_example/ETclassAltLines.txt"#
-ETalt <- readLines(ETaltfile)#
-ETsampleNames <- ETalt[seq(1, length(ETalt), 2)]#
-ETvalues      <- ETalt[seq(2, length(ETalt), 2)]#
-cbind(samples=ETsampleNames, enterotype=ETvalues)
-partialET <- cbind(samples=ETsampleNames, enterotype=ETvalues)
-write.table(partialET, "~/Dropbox/R/enterotype_example/partialET.txt", quote=FALSE, sep="\t")
-write.table(partialET, "~/Dropbox/R/enterotype_example/partialET.txt", quote=FALSE, sep="\t", row.names=FALSE)
-read.table(etfile)
-etfile <- "~/Dropbox/R/enterotype_example/ET_class_tab.txt"
-read.table(etfile)
-read.table(etfile, header=TRUE)
-et
-et <- read.table(etfile, header=TRUE)
-class(et)
-row.names(et) <- et$Subject
-head(et)
-sampleMap(et)
-etSM <- sampleMap(et)
-sample.names(etSM)
-intersect(sample.names(MHS), sample.names(etSM))
-# Now import into phyloseq#
-library("phyloseq")#
-MHS <- otuTable(MHsanger, TRUE)#
-MHI <- otuTable(MHillumi, TRUE)#
-TPS <- otuTable(Tpyroseq, TRUE)
-intersect(sample.names(MHS), sample.names(etSM))
-sample.names(MHS)
-OTU <- merge_phyloseq(MHS, MHI, TPS)
-intersect(sample.names(OTU), sample.names(etSM))
-sample.names(OTU)
-Tpyroseq
-TPS
-Tpyroseq
 colnames(Tpyroseq)
 MHsangerFN <- "~/Dropbox/R/enterotype_example/phylo_tables/MetaHIT_41SangerSamples.genus.txt"#
 MHillumiFN <- "~/Dropbox/R/enterotype_example/phylo_tables/MetaHIT_85IlluminaSamples.genus.txt"#
@@ -569,3 +325,77 @@ df
 dim(combn(130, 2))
 dim(combn(130, 2))[2]
 dim(combn(nsamples(sg), 2))[2]/dim(combn(130, 2))[2]
+library("phyloseq")
+bigTree <- read.tree("~/Downloads/Caporaso_Data/gg_tree/gg_97_otus_4feb2011.tre")
+bigTree
+data(GlobalPatterns)
+all( species.names(GlobalPatterns) %in% species.names(bigTree) )
+species.names(GlobalPatterns)
+all( species.names(bigTree)        %in% species.names(GlobalPatterns) )
+all( species.names(GlobalPatterns) %in% species.names(bigTree) )
+all( species.names(GlobalPatterns) %in% species.names(bigTree) )
+all( species.names(GlobalPatterns) %in% species.names(bigTree) )
+bigTree
+GlobalPatterns2 <- merge_phyloseq(GlobalPatterns, bigTree)
+GlobalPatterns2
+GlobalPatterns
+cat("installing Bioconductor dependencies for local build \n")
+cat("installing Bioconductor version of phyloseq \n")
+source("https://github.com/downloads/joey711/phyloseq/phyloseq_install_github.R")
+global_patterns_file2 <- "~/Downloads/mcmurdie/gaiix_pnas/GlobalPatterns2.RData"#
+save(GlobalPatterns2, file=global_patterns_file2)
+global_patterns_file2 <- "~/Downloads/Caporaso_Data/gaiix_pnas/GlobalPatterns2.RData"
+save(GlobalPatterns2, file=global_patterns_file2)
+GlobalPatterns2
+?UniFrac
+library("doParallel")
+registerDoParallel(cores=6)
+library("doParallel")#
+registerDoParallel(cores=6)#
+system.time(GPUF <- UniFrac(GlobalPatterns2, parallel=TRUE))#
+#
+## Documentation source for gobal-patterns data
+456.558/60
+?source
+install_github
+library(devtools)
+install_github
+GPUF
+global_patterns_UF_file <- "~/Downloads/Caporaso_Data/gaiix_pnas/Unweighted_UniFrac.RData"
+global_patterns_UF_file <- "~/Downloads/Caporaso_Data/gaiix_pnas/Unweighted_UniFrac.RData"
+save(GPUF, file=global_patterns_UF_file)
+MovingPicturesDataFile <- "~/Downloads/mcmurdie/moving_pictures/MovingPictures.RData"
+load(MovingPicturesDataFile)
+MovingPicturesDataFile <- "~/Downloads/Caporaso_Data/moving_pictures/MovingPictures.RData"
+load(MovingPicturesDataFile)
+all( species.names(MovingPictures) %in% species.names(bigTree) )
+all( species.names(bigTree)        %in% species.names(MovingPictures) )
+nspecies(MovingPictures)
+system.time(MovingPictures2 <- merge_phyloseq(MovingPictures, bigTree))
+MovingPictures2
+MovingPicturesDataFile
+MovingPictures
+MovingPictures <- MovingPictures2
+MovingPictures
+save(MovingPictures, file=MovingPicturesDataFile)
+MovingPictures
+GlobalPatterns
+GlobalPatterns2
+all.equal(GlobalPatterns, phyloseq(otuTable(GlobalPatterns2), sampleData(GlobalPatterns2), taxTab(GlobalPatterns2)))
+global_patterns_file <- "~/Downloads/mcmurdie/gaiix_pnas/GlobalPatterns.RData"
+GlobalPatterns
+GlobalPatterns2
+GlobalPatterns <- GlobalPatterns2
+global_patterns_file <- "~/Downloads/Caporaso_Data/gaiix_pnas/GlobalPatterns.RData"
+global_patterns_file
+save(GlobalPatterns, file=global_patterns_file)
+getVariable(GlobalPatterns, "SampleType")
+variable.names
+variable.names(GlobalPatterns)
+sample.variables(GlobalPatterns)
+sample.variables(GlobalPatterns)
+??"ranks"
+print(GlobalPatterns)
+tre
+getMethod(tre, "character")
+getMethod(tre, signature("character"))

data/datalist

@@ -0,0 +1,5 @@
+GlobalPatterns
+enterotype
+esophagus
+ex1
+soilrep

inst/NEWS

@@ -3,11 +3,17 @@ phyloseq 0.99.x
 * Bioconductor development release updates.
 * BIOM format import: import_biom() function
 * Parallel Fast UniFrac
+* Several published exampled datasets included
 * Directly call vegdist() on phyloseq-class object (method extension)
 * General importer for all supported data formats: import()
 * Lots of documentation updates.
 * Lots and lots of fixes and improvements.
 
+v0.99.23
+===========
+* Added a rooted tree to "GlobalPatterns" dataset
+* Allow multi-class tests with mt()
+
 v0.99.20
 ===========
 * Added "GlobalPatterns" dataset, and some other minor improvements