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--- output: md_document: variant: markdown_github html_preview: false --- <!-- is generated from README.Rmd. Please edit that file --> # ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data ```{r echo=FALSE, results="hide", message=FALSE} #library("txtplot") library("badger") library("ypages") library("ggplot2") library("yyplot") ``` <img src="" height="200" align="right" /> `r badge_bioc_release("ggtree", "green")` `r badge_devel("guangchuangyu/ggtree", "green")` [![Bioc](]( [![Awesome](]( [![Say Thanks!](!-1EAEDB.svg)]( [![platform](]( [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](]( [![codecov](]( [![Last-changedate](`r gsub('-', '--', Sys.Date())`-green.svg)]( [![GitHub forks](]( [![GitHub stars](]( The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. [![Twitter](]( For details, please visit our project website, <>. + [Documentation]( + [FAQ]( + [Featured Articles]( + [Feedback]( ----------------------------------------------------- Please cite the following article when using `ggtree`: __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36. `r badge_doi("10.1111/2041-210X.12628", "green")` `r badge_altmetric("10533079", "green")` `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")` ---------------------------------------------------------------------------------------- ### Citation ```{r echo=F, comment=NA} p <- plot_citation_trend('DO5oG40AAAAJ', 'HtEfBTGE9r8C') ggsave(p, file="docs/images/citation.png", width=8, height=4) ``` <img src="docs/images/citation.png" width="890"/> ### Download stats `r badge_download_bioc("ggtree")` `r badge_bioc_download("ggtree", "total", "blue")` `r badge_bioc_download("ggtree", "month", "blue")` ```{r echo=F, message=F, comment=NA} x <- dlstats::bioc_stats("ggtree") x <- x[-nrow(x), ] # last month data is not complete ## txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25) p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() + theme_minimal() +xlab(NULL) + ylab(NULL) + labs(title="ggtree", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor") ggsave(p, file="docs/images/dlstats.png", width=8, height=4) ``` <img src="docs/images/dlstats.png" width="890"/>