## ----style, echo=FALSE, results="asis", message=FALSE------------------------- knitr::opts_chunk$set(tidy = FALSE, message = FALSE) ## ----echo=FALSE--------------------------------------------------------------- CRANpkg <- function (pkg) { cran <- "https://CRAN.R-project.org/package" fmt <- "[%s](%s=%s)" sprintf(fmt, pkg, cran, pkg) } Biocpkg <- function (pkg) { sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg) } ## ----treeman, echo=FALSE, out.extra='', message=FALSE------------------------- treeman <- matrix(c( "collapse", "collapse a selecting clade", "expand", "expand collapsed clade", "flip", "exchange position of 2 clades that share a parent node", "groupClade", "grouping clades", "groupOTU", "grouping OTUs by tracing back to most recent common ancestor", "identify", "interactive tree manipulation", "rotate", "rotating a selected clade by 180 degree", "rotate_tree", "rotating circular layout tree by specific angle", "scaleClade", "zoom in or zoom out selecting clade", "open_tree", "convert a tree to fan layout by specific open angle" ), ncol=2, byrow=TRUE) treeman <- as.data.frame(treeman) colnames(treeman) <- c("Function", "Descriptiotn") knitr::kable(treeman, caption = "Tree manipulation functions.", booktabs = T) ## ----geoms, echo=FALSE, message=FALSE----------------------------------------- geoms <- matrix(c( "geom_balance", "highlights the two direct descendant clades of an internal node", "geom_cladelabel", "annotate a clade with bar and text label", "geom_cladelabel2", "annotate a clade with bar and text label for unrooted layout", "geom_hilight", "highlight a clade with rectangle", "geom_hilight_encircle", "highlight a clade with xspline for unrooted layout", "geom_label2", "modified version of geom_label, with subsetting supported", "geom_nodelab", "layer for node labels, which can be text or image", "geom_nodepoint", "annotate internal nodes with symbolic points", "geom_point2", "modified version of geom_point, with subsetting supported", "geom_range", "bar layer to present uncertainty of evolutionary inference", "geom_rootpoint", "annotate root node with symbolic point", "geom_segment2", "modified version of geom_segment, with subsetting supported", "geom_strip", "annotate associated taxa with bar and (optional) text label", "geom_taxalink", "associate two related taxa by linking them with a curve", "geom_text2", "modified version of geom_text, with subsetting supported", "geom_tiplab", "layer of tip labels, which can be text or image", "geom_tiplab2", "layer of tip labels for circular layout", "geom_tippoint", "annotate external nodes with symbolic points", "geom_tree", "tree structure layer, with multiple layout supported", "geom_treescale", "tree branch scale legend" ), ncol=2, byrow=TRUE) geoms <- as.data.frame(geoms) colnames(geoms) <- c("Layer", "Description") knitr::kable(geoms, caption = "Geom layers defined in ggtree.", booktabs = T)