Customise taxa and constraint labels on your ordination plots.
Choose 'text' or 'label' type, rotate and/or justify the text/labels
and set aesthetic appearances using tax_lab_style() or
constraint_lab_style().
tax_lab_style(
type = "label",
max_angle = 0,
perpendicular = FALSE,
aspect_ratio = 1,
justify = "auto",
size = 2,
alpha = 1,
colour = "black",
...
)
constraint_lab_style(
type = "label",
max_angle = 0,
perpendicular = FALSE,
aspect_ratio = 1,
justify = "auto",
size = 2.5,
alpha = 1,
colour = "brown",
...
)Arguments
- type
'label', 'text' or 'richtext' ('richtext' also used if 'label' type are rotated, when max_angle > 0)
- max_angle
maximum angle of rotation to allow to match vector angle (requires ggtext package to rotate "label" type)
- perpendicular
if TRUE, sets rotated labels perpendicular to desired angle, not parallel
- aspect_ratio
aspect ratio of plot (y/x) must also be used in coord_fixed() ratio argument (must be set when rotated labels are used, to ensure match to arrow angles)
- justify
"center", "side", or "auto"? Should the text/label align with the arrows at the text center or text sides (uses hjust, if 'auto', picks based on whether max_angle is greater than 0)
- size
fixed size of text or label
- alpha
fixed alpha of text or label
- colour
fixed colour of text or label
- ...
further named arguments passed to geom_text, geom_label or geom_richtext
Value
named list
Examples
# These examples show styling of taxa labels with tax_lab_style().
# The same options are available for constraint labels in constrained
# ordinations. constraint_lab_style() just has different default settings.
library(ggplot2)
# get example inflammatory bowel disease stool dataset from corncob package
data("ibd", package = "microViz")
# filter out rare taxa and clean up names etc
ibd <- ibd %>%
tax_filter(min_prevalence = 3) %>%
tax_fix() %>%
phyloseq_validate()
# calculate a centered-log-ratio transformed PCA ordination
ibd_ord <- ibd %>%
tax_transform("clr", rank = "Genus") %>%
ord_calc("PCA")
# basic plot with default label style
ibd_ord %>% ord_plot(color = "ibd", plot_taxa = 1:10)
# Rotating labels: requires the ggtext package #
# A fixed coordinate ratio must be set to ensure label rotation
# matches the vectors. It is also helpful to set the vector and label length
# multipliers manually for a good look. Rotated labels are justified to the
# 'sides' automatically by tax_lab_style() with justify = 'auto'
ibd_ord %>%
ord_plot(
color = "ibd", plot_taxa = 1:7,
tax_vec_length = 1.3, tax_lab_length = 1.3,
tax_lab_style = tax_lab_style(max_angle = 90)
) +
coord_fixed(ratio = 1, clip = "off", xlim = c(-3.5, 3.5))
# You can use text instead of labels
# - a bold fontface helps text to stand out
# - see ?ggplot2::geom_text for all settings available
ibd_ord %>%
ord_plot(
color = "ibd", plot_taxa = 1:7,
tax_vec_length = 1.3, tax_lab_length = 1.4,
tax_lab_style = tax_lab_style(
type = "text", max_angle = 90, size = 2.5, fontface = "bold.italic"
)
) +
coord_fixed(ratio = 1, clip = "off", xlim = c(-3.5, 3.5))
# With text you can prevent overlaps with check_overlap = TRUE
ibd_ord %>%
ord_plot(
color = "ibd", plot_taxa = 1:12,
tax_vec_length = 1.3, tax_lab_length = 1.4,
tax_lab_style = tax_lab_style(
type = "text", max_angle = 90, size = 3, fontface = "bold.italic",
check_overlap = TRUE
)
) +
coord_fixed(ratio = 1, clip = "off", xlim = c(-3.5, 3.5))
# With labels, you can reduce the padding and line weight to free space
# but check_overlap is not available
# see ?ggtext::geom_richtext for more possibilities
ibd_ord %>%
ord_plot(
color = "ibd", plot_taxa = 1:7,
tax_vec_length = 1.3, tax_lab_length = 1.35,
tax_lab_style = tax_lab_style(
max_angle = 90, fontface = "italic", size = 2.5, fill = "grey95",
label.size = 0.1, # width outline
label.padding = unit(0.1, "lines"),
label.r = unit(0, "lines") # reduces rounding of corners to radius 0
)
) +
coord_fixed(ratio = 1, clip = "off", xlim = c(-3.5, 3.5))
# Perpendicular angled labels/text are possible
ibd_ord %>%
ord_plot(
color = "ibd", plot_taxa = 1:12,
tax_lab_style = tax_lab_style(
type = "text", max_angle = 90, perpendicular = TRUE, size = 3,
check_overlap = TRUE
)
) +
coord_fixed(ratio = 1, clip = "off", xlim = c(-3.5, 3.5))
# You can limit and/or attenuate the angle of rotation by:
# - setting a lower max_angle
# - decreasing the aspect_ratio in the tax_lab_style call
ibd_ord %>%
ord_plot(
shape = "circle", color = "ibd", plot_taxa = 1:7,
tax_vec_length = 1.3, tax_lab_length = 1.3,
tax_lab_style = tax_lab_style(
max_angle = 10, size = 2, label.size = 0.1,
label.padding = unit(0.1, "lines"), label.r = unit(0, "lines")
)
) +
coord_fixed(ratio = 1, clip = "off", xlim = c(-3.5, 3.5))
ibd_ord %>%
ord_plot(
shape = "circle", color = "ibd", plot_taxa = 1:7,
tax_vec_length = 1.3, tax_lab_length = 1.3,
tax_lab_style = tax_lab_style(
max_angle = 90, size = 2, label.size = 0.1, aspect_ratio = 0.5,
label.padding = unit(0.1, "lines"), label.r = unit(0, "lines")
)
) +
coord_fixed(ratio = 1, clip = "off", xlim = c(-3.5, 3.5))
# another example with some extras #
ibd_ord %>%
ord_plot(
shape = "circle filled", fill = "ibd",
plot_taxa = 1:10,
taxon_renamer = function(x) stringr::str_replace_all(x, "_", " "),
tax_vec_length = 2, tax_lab_length = 2.1,
tax_lab_style = tax_lab_style(
type = "text", max_angle = 90, size = 2.5,
fontface = "bold.italic", check_overlap = TRUE
)
) +
coord_fixed(1, clip = "off", xlim = c(-5, 5)) +
theme(legend.position = c(0.8, 0.2), legend.background = element_rect()) +
stat_chull(mapping = aes(colour = ibd, fill = ibd), alpha = 0.1)
#> Warning: A numeric `legend.position` argument in `theme()` was deprecated in ggplot2
#> 3.5.0.
#> ℹ Please use the `legend.position.inside` argument of `theme()` instead.
