geom_axis: Axes through the origin

In corybrunson/ordr: A Tidyverse Extension for Ordinations and Biplots

Axes through the origin

Description

geom_axis() renders lines through the origin and the position of each case or variable.

Usage

geom_axis(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  axis_labels = TRUE,
  axis_ticks = TRUE,
  axis_text = TRUE,
  by = NULL,
  num = NULL,
  tick_length = 0.025,
  text_dodge = 0.03,
  label_dodge = 0.03,
  ...,
  parse = FALSE,
  check_overlap = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping	Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
data	The data to be displayed in this layer. There are three options: If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot(). A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created. A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).
stat	The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")
position	Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
axis_labels, axis_ticks, axis_text	Logical; whether to include labels, tick marks, and text value marks along the axes.
by, num	Intervals between elements or number of elements; specify only one.
tick_length	Numeric; the length of the tick marks, as a proportion of the minimum of the plot width and height.
text_dodge	Numeric; the orthogonal distance of the text from the axis, as a proportion of the minimum of the plot width and height.
label_dodge	Numeric; the orthogonal distance of the text from the axis or isoline, as a proportion of the minimum of the plot width and height.
...	Additional arguments passed to ggplot2::layer().
parse	If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.
check_overlap	If TRUE, text that overlaps previous text in the same layer will not be plotted. check_overlap happens at draw time and in the order of the data. Therefore data should be arranged by the label column before calling geom_text(). Note that this argument is not supported by geom_label().
na.rm	Passed to ggplot2::layer().
show.legend	logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

Value

A ggproto layer.

Biplot layers

ggbiplot() uses ggplot2::fortify() internally to produce a single data frame with a .matrix column distinguishing the subjects ("rows") and variables ("cols"). The stat layers stat_rows() and stat_cols() simply filter the data frame to one of these two.

The geom layers ⁠geom_rows_*()⁠ and ⁠geom_cols_*()⁠ call the corresponding stat in order to render plot elements for the corresponding factor matrix. ⁠geom_dims_*()⁠ selects a default matrix based on common practice, e.g. points for rows and arrows for columns.

Aesthetics

geom_axis() understands the following aesthetics (required aesthetics are in bold):

• x

• y

• colour

• alpha

• linewidth

• linetype

• label

• center, scale

• label_colour, label_alpha, label_size, label_angle, label_hjust, label_vjust, label_family, label_fontface

• tick_colour, tick_alpha, tick_linewidth, tick_linetype

• text_colour, text_alpha, text_size, text_angle, text_hjust, text_vjust, text_family, text_fontface

• group

The prefixed aesthetics ⁠label_*⁠, ⁠tick_*⁠, and ⁠text_*⁠ are used by the text elements and will inherit any values passed to their un-prefixed counterparts, if recognized.

See Also

Other geom layers: geom_isoline(), geom_lineranges(), geom_origin(), geom_text_radiate(), geom_vector()

Examples

# Freestone primary glass measurements
print(glass)

# default (standardized) linear discriminant analysis of sites on measurements
glass_lda <- MASS::lda(Site ~ SiO2 + Al2O3 + FeO + MgO + CaO, glass)
# bestow 'tbl_ord' class & augment observation, centroid, and variable fields
as_tbl_ord(glass_lda) %>%
  augment_ord() %>%
  mutate_rows(discriminant =
                ifelse(.element == "active", "centroid", "case")) %>%
  print() -> glass_lda
# row-standard biplot
glass_lda %>%
  confer_inertia(1) %>%
  ggbiplot() +
  theme_bw() + theme_biplot() +
  geom_rows_point(aes(shape = grouping, size = discriminant), alpha = .5) +
  geom_cols_axis(aes(label = name), color = "#888888", num = 8L,
                 text_size = 2.5, label_dodge = .02) +
  scale_shape_manual(values = c(2L, 3L, 0L, 5L)) +
  ggtitle(
    "LDA of Freestone glass measurements",
    "Row-standard biplot of standardized LDA"
  )

# contribution LDA of sites on measurements
glass_lda <-
  lda_ord(Site ~ SiO2 + Al2O3 + FeO + MgO + CaO, glass,
          axes.scale = "contribution")
# bestow 'tbl_ord' class & augment observation, centroid, and variable fields
as_tbl_ord(glass_lda) %>%
  augment_ord() %>%
  mutate_rows(discriminant =
                ifelse(.element == "active", "centroid", "case")) %>%
  print() -> glass_lda
# symmetric biplot
glass_lda %>%
  confer_inertia(.5) %>%
  ggbiplot() +
  theme_bw() + theme_biplot() +
  geom_rows_point(aes(shape = grouping, alpha = discriminant)) +
  geom_cols_axis(color = "#888888", num = 8L,
                 text_size = 2.5, text_dodge = .025) +
  scale_shape_manual(values = c(16L, 17L, 15L, 18L)) +
  ggtitle(
    "LDA of Freestone glass measurements",
    "Symmetric biplot of contribution LDA"
  )

corybrunson/ordr documentation built on Feb. 15, 2024, 9:28 p.m.