Added support for XStringSet in msaplot

[yasche]

Description

Added support for XStringSet objects (i.e., BStringSet, AAStringSet and DNAStringSet) for function msaplot() in response to #626. The problem came up because an old example on R-Bloggers does not work anymore.

In the proposed solution, if the object is of type BStringSet it is first checked, if library Biostrings is installed. If so, a temporary file is created and read via treeio::read.fasta() to circumvent the need to check if it as amino acid or DNA sequence. Otherwise it throws a helpful error message. AAStringSet and DNAStringSet objects are converted using functions from the ape package.

Tests

library(ggtree) library(Biostrings) library(phyloseq) library(ggplot2) library(scales) data(GlobalPatterns) GP <- prune_taxa(taxa_sums(GlobalPatterns) > 0, GlobalPatterns) GP.chl <- subset_taxa(GP, Phylum=="Chlamydiae") p <- ggtree(GP.chl, ladderize = FALSE) + geom_text2(aes(subset=!isTip, label=label), hjust=-.2, size=4) + geom_tiplab(aes(label=Genus), hjust=-.3) + geom_point(aes(x=x+hjust, color=SampleType, shape=Family, size=Abundance),na.rm=TRUE) + scale_size_continuous(trans=log_trans(5)) + theme(legend.position="right") df <- fortify(GP.chl) barcode <- as.character(df$Barcode_full_length) names(barcode) <- df$label barcode <- barcode[!is.na(barcode)] #With Biostrings installed ##XStringSets bss_barcode <- Biostrings::BStringSet(barcode) p1 <- p + ggtitle("reproduce phyloseq by ggtree, BStringSet") msaplot(p1, bss_barcode, width=.3, offset=.05) ggsave("plots/bss.svg", height = 9) aass_barcode <- AAStringSet(bss_barcode) p2 <- p + ggtitle("reproduce phyloseq by ggtree, AAStringSet") msaplot(p2, aass_barcode, width=.3, offset=.05) ggsave("plots/aass.svg", height = 9) dnass_barcode <- DNAStringSet(bss_barcode) p3 <- p + ggtitle("reproduce phyloseq by ggtree, DNAStringSet") msaplot(p3, dnass_barcode, width=.3, offset=.05) ggsave("plots/dnass.svg", height = 9) ##XXX.bin aabin_barcode <- ape::as.AAbin(aass_barcode) p4 <- p + ggtitle("reproduce phyloseq by ggtree, AABin") msaplot(p4, aabin_barcode, width=.3, offset=.05) ggsave("plots/aabin.svg", height = 9) dnabin_barcode <- ape::as.DNAbin(dnass_barcode) p5 <- p + ggtitle("reproduce phyloseq by ggtree, DNABin") msaplot(p5, dnabin_barcode, width=.3, offset=.05) ggsave("plots/dnabin.svg", height = 9) ##file writeXStringSet(bss_barcode, "fastafile.fasta") p6 <- p + ggtitle("reproduce phyloseq by ggtree, file") msaplot(p6, "fastafile.fasta", width=.3, offset=.05) ggsave("plots/file.svg", height = 9) #Without Biostrings installed unloadNamespace("phyloseq") unloadNamespace("Biostrings") remove.packages("Biostrings") ##XStringSet a <- list("ABC") class(a) <- "BStringSet" p7 <- p + ggtitle("reproduce phyloseq by ggtree, BStringSet without Biostrings") msaplot(p7, a, width=.3, offset=.05) #Error in msaplot(p7, a, width = 0.3, offset = 0.05) : #object is of class 'BStringSet' but library 'Biostrings' is not installed... #-> please install 'Biostrings' from https://bioconductor.org/packages/Biostrings for handling objects of type 'BStringSet'. 

The function produces the expected outcome:

[GuangchuangYu]

thanks.