C Figures and Tables

TABLE C.1: Geometric layers that supported by `geom_facet()’
Package Geom Layer Description
ggalt geom_dumbbell creates dumbbell charts
ggbio geom_alignment shows interval data as alignment
ggfittext geom_fit_text 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
ggimage geom_phylopic queries image files from the PhyloPic database and visualizes them
ggplot2 geom_hline adds horizontal lines
ggplot2 geom_jitter adds a small amount of random variation to the location of each point
ggplot2 geom_label draws a rectangle behind the text
ggplot2 geom_point creates scatterplots
ggplot2 geom_raster a high-performance special case for all the tiles that are the same size
ggplot2 geom_rect draws rectangle by using the locations of the four corners
ggplot2 geom_segment draws a straight line between points
ggplot2 geom_spoke a polar parameterization of ‘geom_segment()’
ggplot2 geom_text adds text to the plot
ggplot2 geom_tile draws rectangle by using the center of the tile and its size
ggplot2 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
ggrepel 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
ggridges geom_density_ridges_gradient works just like ‘geom_density_ridges’ except that the ‘fill’ aesthetic can vary along the x-axis
ggridges geom_ridgeline plots the sum of the ‘y’ and ‘height’ aesthetics vs. ‘x’, filling the area between ‘y’ and ‘y + height’ with a color
ggridges 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()’
ggstance geom_boxploth horizontal version of ‘geom_boxplot()’
ggstance geom_crossbarh horizontal version of ‘geom_crossbar()’
ggstance geom_errorbarh horizontal version of ‘geom_errorbarh()’
ggstance geom_histogramh horizontal version of ‘geom_histogram()’
ggstance geom_linerangeh horizontal version of ‘geom_linerange()’
ggstance geom_pointrangeh horizontal version of ‘geom_pointrange()’
ggstance geom_violinh horizontal version of ‘geom_violin()’
ggtree geom_motif draws aligned motifs
TABLE C.2: Tree-like objects supported by ggtree
Package Object Description
ape phylo basic phylogenetic tree structure
ape multiPhylo list of phylo objects
ade4 phylog tree structure for ecological data
phylobase phylo4 S4 version of phylo object
phylobase 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
treeio jplace treedata object with placement information
stats hclust hierarchical cluster result
stats dendrogram hierarchical clustering or classification/regression tree
cluster agnes agglomerative hierarchical clustering
cluster diana divisive hierarchical clustering
cluster 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)