taxatree_plotkey: Draw labelled key to accompany taxatree_plots

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Draw labelled key to accompany taxatree_plots

Description

Draw labelled key to accompany taxatree_plots

Usage

taxatree_plotkey(
  data,
  ...,
  size_stat = list(prevalence = prev),
  node_size_range = c(1.5, 5),
  edge_width_range = node_size_range * 0.8,
  size_guide = "none",
  size_trans = "identity",
  colour = "lightgrey",
  edge_alpha = 0.7,
  title = "Key",
  title_size = 14,
  taxon_renamer = identity,
  .combine_label = any,
  .draw_label = TRUE,
  .calc_label = TRUE,
  layout = "tree",
  layout_seed = NA,
  circular = identical(layout, "tree"),
  node_sort = NULL,
  add_circles = isTRUE(circular),
  drop_ranks = TRUE
)

Arguments

data	psExtra (or phyloseq)
...	logical conditions for labelling e.g. rank == "Phylum", p.value < 0.1 | taxon %in% listOfTaxa
size_stat	named list of length 1, giving function calculated for each taxon, to determine the size of nodes (and edges). Name used as size legend title.
node_size_range	min and max node sizes, decrease to avoid node overlap
edge_width_range	min and max edge widths
size_guide	guide for node sizes, try "none", "legend" or ggplot2::guide_legend()
size_trans	transformation for size scale you can use (the name of) any transformer from the scales package, such as "identity", "log1p", or "sqrt"
colour	fixed colour and fill of nodes and edges
edge_alpha	fixed alpha value for edges
title	title of plot (NULL for none)
title_size	font size of title
taxon_renamer	function that takes taxon names and returns modified names for labels
.combine_label	all or any: function to combine multiple logical "label" values for a taxon (relevant if taxatree_stats already present in data)
.draw_label	should labels be drawn, or just the bare tree, set this to FALSE if you want to draw customised labels with taxatree_plot_labels afterwards
.calc_label	if you already set labels with taxatree_label: set this to FALSE to use / avoid overwriting that data (ignores ... if FALSE)
layout	any ggraph layout, default is "tree"
layout_seed	any numeric, required if a stochastic igraph layout is named
circular	should the layout be circular?
node_sort	sort nodes by "increasing" or "decreasing" size? NULL for no sorting. Use tax_sort() before taxatree_plots() for finer control.
add_circles	add faint concentric circles to plot, behind each rank?
drop_ranks	drop ranks from tree if not included in stats dataframe

Value

ggplot

Examples

library(ggplot2)
# Normally you make a key to accompany taxatree_plots showing stats results
# So see ?taxatree_plots examples too!
#
# You can also use the taxatree key visualization just to help understand your
# tax_table contents and hierarchical structure
shao19 %>%
  ps_filter(family_id %in% 1:5) %>%
  tax_filter(min_prevalence = 7) %>%
  tax_fix() %>%
  tax_agg("genus") %>%
  tax_prepend_ranks() %>%
  taxatree_plotkey(rank %in% c("phylum", "genus"))


# # Let's look at some of the most prevalent Actinobacteria
actinoOnlyPhylo <- shao19 %>%
  tax_select("Actinobacteria", ranks_searched = "phylum") %>%
  tax_filter(min_prevalence = 100)

actinoOnlyPhylo %>%
  tax_mutate(order = NULL) %>%
  tax_sort(by = "prev", at = "species", tree_warn = FALSE) %>%
  taxatree_plotkey(
    circular = FALSE, rank != "genus",
    .draw_label = FALSE, # suppress drawing now so we can make custom labels after
    size_guide = "legend", colour = "skyblue", edge_alpha = 0.2
  ) %>%
  taxatree_plot_labels(
    circular = FALSE, # be sure you match the plotkey layout
    fun = geom_text, fontface = "bold.italic", size = 2.5, hjust = 0,
    nudge_y = 0.1 # nudge y if you want to nudge x (due to coord_flip!)
  ) +
  coord_flip(clip = "off") +
  scale_y_reverse(expand = expansion(add = c(0.2, 2))) +
  theme(legend.position = c(0.15, 0.25), legend.background = element_rect())


# You can even choose other tree layouts from igraph (e.g. kk)
# and configure multiple styles of custom labels on one plot
set.seed(1) # set seed for reproducibility of ggrepel label positions
actinoOnlyPhylo %>%
  tax_mutate(order = NULL) %>%
  taxatree_label(rank == "family", .label_var = "family_lab") %>%
  taxatree_label(rank == "species", .label_var = "species_lab") %>%
  taxatree_plotkey(
    circular = FALSE, rank != "genus", layout = "kk",
    .draw_label = FALSE, # important not to draw the default labels
    colour = "skyblue", edge_alpha = 0.2
  ) %>%
  taxatree_plot_labels(
    circular = FALSE, label_var = "family_lab", fun = geom_label,
    fontface = "bold.italic", colour = "orange", fill = "black", size = 3
  ) %>%
  taxatree_plot_labels(
    circular = FALSE, label_var = "species_lab", fun = ggrepel::geom_text_repel,
    fontface = "bold.italic", size = 2, force = 20, max.time = 0.1
  )

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.