fixed plot_phyloseq checking for wrong slots ...

R/IO-methods.R

@@ -350,7 +350,7 @@ import_qiime <- function(otufilename=NULL, mapfilename=NULL,
 #' read_tree(system.file("extdata", "GP_tree_rand_short.newick.gz", package="phyloseq"))
 read_tree <- function(treefile, errorIfNULL=FALSE, ...){
 	# "phylo" object provided directly
-	if( class(treefile)[1] %in% c("phylo") ){ 
+	if( is(treefile, "phylo") ){ 
 		tree <- treefile
 	} else {
 	  # file path to tree file provided.
@@ -637,7 +637,7 @@ import_env_file <- function(envfilename, tree=NULL, sep="\t", ...){
 	# Convert to otu_table-class table (trivial table)
 	physeq <- envHash2otu_table(tipSampleTable)
 	# If tree is provided, combine it with the OTU Table
-	if( class(tree) == "phylo" ){
+	if( is(tree, "phylo") ){
 		# Create phyloseq-class with a tree and OTU Table (will perform any needed pruning)
 		physeq <- phyloseq(physeq, tree)
 	}
@@ -1472,8 +1472,8 @@ import_mothur_dist <- function(mothur_dist_file){
 #' myDistObject <- as.dist(ape::cophenetic.phylo(phy_tree(esophagus)))
 #' export_mothur_dist(myDistObject)
 export_mothur_dist <- function(x, out=NULL, makeTrivialNamesFile=NULL){
-	if( class(x)== "matrix" ){ x <- as.dist(x) }
-	if( class(x)!= "dist" ){ stop("x must be a dist object, or symm matrix") }
+	if( is.matrix(x) ){ x <- as.dist(x) }
+	if( !is(x, "dist") ){ stop("x must be a dist object, or symm matrix") }
 
 	# While x is a dist-object, get the length of unique pairs
 	# to initialize the dist table.
@@ -1769,9 +1769,9 @@ import_biom <- function(BIOMfilename,
 	argumentlist <- list()
 
 	# Read the data
-	if(class(BIOMfilename)=="character"){
+	if( is.character(BIOMfilename) ){
 		x = read_biom(biom_file=BIOMfilename)
-	} else if (class(BIOMfilename)=="biom"){
+	} else if (is(BIOMfilename, "biom")){
 		x = BIOMfilename
 	} else {
 		stop("import_biom requires a 'character' string to a biom file or a 'biom-class' object")

R/merge-methods.R

@@ -235,7 +235,7 @@ setMethod("merge_phyloseq_pair", signature("phylo", "phylo"), function(x, y){
 #' @aliases merge_phyloseq_pair,XStringSet,XStringSet-method
 #' @rdname merge_phyloseq_pair-methods
 setMethod("merge_phyloseq_pair", signature("XStringSet", "XStringSet"), function(x, y){
-	if( class(x) != class(y) ){
+	if( is(x, class(y)) ){
 		# if class of x and y don't match, throw warning, try anyway (just in case)
 		warning("For merging reference sequence objects, x and y should be same type.\n",
 			"That is, the same subclass of XStringSet. e.g. both DNAStringSet.\n", 
@@ -522,11 +522,11 @@ setMethod("merge_samples", signature("sample_data"), function(x, group, fun=mean
 	x1    <- data.frame(x)
 
 	# Check class of group and modify if "character"
-	if( class(group)=="character" & length(group)==1 ){
+	if( is.character(group) & length(group)==1 ){
 		if( !group %in% colnames(x) ){stop("group not found among sample variable names.")}
 		group <- x1[, group]
 	}
-	if( class(group)!="factor" ){
+	if( !is.factor(group) ){
 		# attempt to coerce to factor
 		group <- factor(group)
 	}
@@ -571,20 +571,20 @@ setMethod("merge_samples", signature("phyloseq"), function(x, group, fun=mean){
 	# Check if phyloseq object has a sample_data
 	if( !is.null(sample_data(x, FALSE)) ){
 		# Check class of group and modify if single "character" (column name)
-		if( class(group)=="character" & length(group)==1 ){
+		if( is.character(group) & length(group)==1 ){
 			x1 <- data.frame(sample_data(x))		
 			if( !group %in% colnames(x1) ){stop("group not found among sample variable names.")}
 			group <- x1[, group]
 		}
 		# coerce to factor
-		if( class(group)!="factor" ){ group <- factor(group) }
+		if( !is.factor(group) ){ group <- factor(group) }
 		# Perform merges.
 		newSM <- merge_samples(sample_data(x), group, fun)
 		newOT <- merge_samples(otu_table(x), group)
 		phyloseqList <- list(newOT, newSM)
 	# Else, the only relevant object to "merge_samples" is the otu_table
 	} else {
-		if( class(group)!="factor" ){ group <- factor(group) }
+		if( !is.factor(group) ){ group <- factor(group) }
 		phyloseqList <- list( newOT=merge_samples(otu_table(x), group) )
 	}
 

R/network-methods.R

@@ -100,7 +100,7 @@ make_network <- function(physeq, type="samples", distance="jaccard", max.dist =
 
 	if( type %in% c("taxa", "species", "OTUs", "otus", "otu")){
     # Calculate or asign taxa-wise distance matrix
-	  if( class(distance) == "dist" ){ 
+	  if( is(distance,"dist") ){ 
 	    # If distance a distance object, use it rather than re-calculate
 	    obj.dist <- distance
 	    if( attributes(obj.dist)$Size != ntaxa(physeq) ){
@@ -109,7 +109,7 @@ make_network <- function(physeq, type="samples", distance="jaccard", max.dist =
 	    if( !setequal(attributes(obj.dist)$Labels, taxa_names(physeq)) ){
 	      stop("taxa_names does not exactly match dist-indices")
 	    }
-	  } else if( class(distance) == "character" ){ 
+	  } else if( is.character(distance) ){ 
 	    # If character string, pass on to distance(), assume supported
 	    obj.dist <- distance(physeq, method=distance, type=type, ...)
 	    # Else, assume a custom function and attempt to calculate.
@@ -127,7 +127,7 @@ make_network <- function(physeq, type="samples", distance="jaccard", max.dist =
 		CoMa <- TaDiMa < max.dist   
 	} else if( type == "samples" ){
     # Calculate or asign sample-wise distance matrix
-	  if( class(distance) == "dist" ){ # If argument is already a distance matrix.
+	  if( is(distance, "dist") ){ # If argument is already a distance matrix.
 	    # If distance a distance object, use it rather than re-calculate
 	    obj.dist <- distance
 	    if( attributes(obj.dist)$Size != nsamples(physeq) ){
@@ -137,7 +137,7 @@ make_network <- function(physeq, type="samples", distance="jaccard", max.dist =
 	      stop("sample_names does not exactly match dist-indices")
 	    }
 	    # If character string, pass on to distance(), assume supported    	
-	  } else if( class(distance) == "character" ){
+	  } else if( is.character(distance) ){
 	    # Else, assume a custom function and attempt to calculate. 
 	    obj.dist <- distance(physeq, method=distance, type=type, ...)
 	  } else { 

R/ordination-methods.R

@@ -215,7 +215,7 @@ ordinate = function(physeq, method="DCA", distance="bray", formula=NULL, ...){
 	# Define ps.dist. Check the class of distance argument is character or dist
 	if( inherits(distance, "dist") ){
 		ps.dist <- distance
-	} else if( class(distance) == "character" ){
+	} else if( is.character(distance) ){
 		# There are some special options for NMDS/metaMDS if distance-method
 		# is supported by vegdist, so check first. If not, just calculate distance	
 		vegdist_methods <- c("manhattan", "euclidean", "canberra", "bray", 
@@ -323,7 +323,7 @@ ordinate = function(physeq, method="DCA", distance="bray", formula=NULL, ...){
 #' plot_ordination(GP, GP.dpcoa, color="SampleType")
 DPCoA <- function(physeq, correction=cailliez, scannf=FALSE, ...){
 	# Check that physeq is a phyloseq-class
-	if(!class(physeq)=="phyloseq"){stop("physeq must be phyloseq-class")}
+	if(!is(physeq, "phyloseq")){stop("physeq must be phyloseq-class")}
 
 	# Remove any OTUs that are absent from all the samples.
 	physeq <- prune_taxa((taxa_sums(physeq) > 0), physeq)

R/plot-methods.R

@@ -45,9 +45,9 @@ setGeneric("plot_phyloseq", function(physeq, ...){ standardGeneric("plot_phylose
 #' @aliases plot_phyloseq,phyloseq-method
 #' @rdname plot_phyloseq-methods
 setMethod("plot_phyloseq", "phyloseq", function(physeq, ...){
-	if( all(c("otu_table", "sample_data", "phy_tree") %in% getslots.phyloseq(physeq)) ){
+	if( all(c("otu_table", "sam_data", "phy_tree") %in% getslots.phyloseq(physeq)) ){
 		plot_tree(esophagus, color="samples")	
-	} else if( all(c("otu_table", "sample_data", "tax_table") %in% getslots.phyloseq(physeq) ) ){
+	} else if( all(c("otu_table", "sam_data", "tax_table") %in% getslots.phyloseq(physeq) ) ){
 		plot_bar(physeq, ...)
 	} else if( all(c("otu_table", "phy_tree") %in% getslots.phyloseq(physeq)) ){
 		plot_tree(esophagus, color="samples")	
@@ -1168,7 +1168,7 @@ rm.na.phyloseq <- function(DF, key.var){
 	# DF[!is.na(DF[, key.var]), ]
 	DF <- subset(DF, !is.na(eval(parse(text=key.var))))
 	# (2) Remove NA from the factor level, if a factor.
-	if( class(DF[, key.var]) == "factor" ){
+	if( is.factor(DF[, key.var]) ){
 		DF[, key.var] <- factor(as(DF[, key.var], "character"))
 	}
 	return(DF)
@@ -2840,4 +2840,4 @@ plot_clusgap = function(clusgap, title="Gap Statistic results"){
 	p = p + ggtitle(title)
 	return(p)
 }
-################################################################################
+################################################################################

R/sampleData-class.R

@@ -138,7 +138,7 @@ subset_samples <- function(physeq, ...){
 	} else {
 		oldDF <- as(sample_data(physeq), "data.frame")
 		newDF <- subset(oldDF, ...)
-		if( class(physeq) == "sample_data" ){
+		if( is(physeq, "sample_data") ){
 			return(sample_data(newDF))
 		} else {
 			sample_data(physeq) <- sample_data(newDF)