Axes through the origin

Source: R/geom-axis.r

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

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.

Examples

# Reaven & Miller overt & chemical diabetes test data and group classification
head(heplots::Diabetes)
#>   relwt glufast glutest instest sspg  group
#> 1  0.81      80     356     124   55 Normal
#> 2  0.95      97     289     117   76 Normal
#> 3  0.94     105     319     143  105 Normal
#> 4  1.04      90     356     199  108 Normal
#> 5  1.00      90     323     240  143 Normal
#> 6  0.76      86     381     157  165 Normal

# default (standardized) linear discriminant analysis of groups on tests
diabetes_lda <- MASS::lda(group ~ ., heplots::Diabetes)
# bestow 'tbl_ord' class & augment observation, centroid, and variable fields
as_tbl_ord(diabetes_lda) %>%
  augment_ord() %>%
  mutate_rows(discriminant = ifelse(
    .element == "active",
    "centroid", "case"
  )) %>%
  print() -> diabetes_lda
#> # A tbl_ord of class 'lda': (148 x 2) x (5 x 2)'
#> # 2 coordinates: LD1 and LD2
#> # 
#> # Rows (principal): [ 148 x 2 | 6 ]
#>      LD1    LD2 |   name          prior counts group…¹
#>                 |   <chr>         <dbl>  <int> <chr>  
#> 1 -1.75   0.400 | 1 Normal        0.524     76 Normal 
#> 2  0.340 -1.38  | 2 Chemical_Di…  0.248     36 Chemic…
#> 3  3.66   0.580 | 3 Overt_Diabe…  0.228     33 Overt_…
#> 4 -1.72   0.663 | 4 1            NA         NA Normal 
#> 5 -2.85   1.30  | 5 2            NA         NA Normal 
#> # … with 143 more rows, 2 more
#> #   variables: .element <chr>,
#> #   discriminant <chr>, and
#> #   abbreviated variable name
#> #   ¹​grouping
#> # 
#> # Columns (standard): [ 5 x 2 | 2 ]
#>         LD1      LD2 |   name    .element
#>                      |   <chr>   <chr>   
#> 1  1.36     -3.78    | 1 relwt   active  
#> 2 -0.0336    0.0366  | 2 glufast active  
#> 3  0.0126   -0.00709 | 3 glutest active  
#> 4 -0.000102 -0.00617 | 4 instest active  
#> 5  0.00424   0.00113 | 5 sspg    active  
# row-standard biplot
diabetes_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) +
  ggtitle(
    "LDA of Reaven & Miller diabetes groups",
    "Row-standard biplot of standardized LDA"
  )
#> Warning: Using size for a discrete variable is not advised.


# contribution LDA of groups on tests
diabetes_lda <-
  lda_ord(group ~ ., heplots::Diabetes, axes.scale = "contribution")
# bestow 'tbl_ord' class & augment observation, centroid, and variable fields
as_tbl_ord(diabetes_lda) %>%
  augment_ord() %>%
  mutate_rows(discriminant = ifelse(
    .element == "active",
    "centroid", "case"
  )) %>%
  print() -> diabetes_lda
#> # A tbl_ord of class 'lda_ord': (148 x 2) x (5 x 2)'
#> # 2 coordinates: LD1 and LD2
#> # 
#> # Rows (principal): [ 148 x 2 | 6 ]
#>      LD1    LD2 |   name          prior counts group…¹
#>                 |   <chr>         <dbl>  <int> <chr>  
#> 1 -1.75   0.400 | 1 Normal        0.524     76 Normal 
#> 2  0.340 -1.38  | 2 Chemical_Di…  0.248     36 Chemic…
#> 3  3.66   0.580 | 3 Overt_Diabe…  0.228     33 Overt_…
#> 4 -1.72   0.663 | 4 1            NA         NA Normal 
#> 5 -2.85   1.30  | 5 2            NA         NA Normal 
#> # … with 143 more rows, 2 more
#> #   variables: .element <chr>,
#> #   discriminant <chr>, and
#> #   abbreviated variable name
#> #   ¹​grouping
#> # 
#> # Columns (standard): [ 5 x 2 | 2 ]
#>       LD1    LD2 |   name    .element
#>                  |   <chr>   <chr>   
#> 1  0.138  -0.384 | 1 relwt   active  
#> 2 -0.274   0.539 | 2 glufast active  
#> 3  0.861   0.288 | 3 glutest active  
#> 4 -0.0134 -0.666 | 4 instest active  
#> 5  0.388  -0.145 | 5 sspg    active  
# symmetric biplot
diabetes_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) +
  ggtitle(
    "LDA of Reaven & Miller diabetes groups",
    "Symmetric biplot of contribution LDA"
  )
#> Warning: Using alpha for a discrete variable is not advised.