shrinks, grows, or wraps text to fit inside a defined rectangular area
gggenes
geom_gene_arrow
draws genes as arrows
ggimage
geom_image
visualizes image files
geom_phylopic
queries image files from the PhyloPic database and visualizes them
ggplot2
geom_hline
adds horizontal lines
geom_jitter
adds a small amount of random variation to the location of each point
geom_label
draws a rectangle behind the text
geom_point
creates scatterplots
geom_raster
a high-performance special case for all the tiles that are the same size
geom_rect
draws rectangle by using the locations of the four corners
geom_segment
draws a straight line between points
geom_spoke
a polar parameterization of 'geom_segment()'
geom_text
adds text to the plot
geom_tile
draws rectangle by using the center of the tile and its size
geom_vline
adds vertical lines
ggrepel
geom_text_repel
adds text to the plot. The text labels repel away from each other and away from the data points
geom_label_repel
draws a rectangle underneath the text. The text labels repel away from each other and away from the data points
ggridges
geom_density_ridges
arranges multiple density plots in a staggered fashion
geom_density_ridges_gradient
works just like 'geom_density_ridges' except that the 'fill' aesthetic can vary along the *x*-axis
geom_ridgeline
plots the sum of the 'y' and 'height' aesthetics vs. 'x', filling the area between 'y' and 'y + height' with a color
geom_ridgeline_gradient
works just like 'geom_ridgeline' except that the 'fill' aesthetic can vary along the *x*-axis
ggstance
geom_barh
horizontal version of 'geom_bar()'
geom_boxploth
horizontal version of 'geom_boxplot()'
geom_crossbarh
horizontal version of 'geom_crossbar()'
geom_errorbarh
horizontal version of 'geom_errorbarh()'
geom_histogramh
horizontal version of 'geom_histogram()'
geom_linerangeh
horizontal version of 'geom_linerange()'
geom_pointrangeh
horizontal version of 'geom_pointrange()'
geom_violinh
horizontal version of 'geom_violin()'
ggtree
geom_motif
draws aligned motifs
Tree-like objects supported by ggtree
Package
Object
Description
ape
phylo
basic phylogenetic tree structure
multiPhylo
list of phylo objects
ade4
phylog
tree structure for ecological data
phylobase
phylo4
S4 version of phylo object
phylo4d
extend phylo4 with trait data
phyloseq
phyloseq
phylogenetic tree with microbiome data
tidytree
tbl_tree
phylogenetic tree as a tidy data frame
treeio
treedata
phylogenetic tree with heterogeneous associated data
jplace
treedata object with placement information
stats
hclust
hierarchical cluster result
dendrogram
hierarchical clustering or classification/regression tree
cluster
agnes
agglomerative hierarchical clustering
diana
divisive hierarchical clustering
twins
agglomerative or divisive (polythetic) hierarchical clustering
pvclust
pvclust
hierarchical clustering with p-values calculated by multiscale bootstrap resampling
igraph
igraph
network (currently only tree graph supported)
18 Session Info
library("yulab.utils")
The book was written using R Markdown and was compiled by bookdown package. Here is the session information on the system on which this thesis was compiled: