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PCA Biplot with ggplot2

Source: R/ggplot_pca.R
ggplot_pca.Rd

Produces a ggplot2 variant of a so-called biplot for PCA (principal component analysis), but is more flexible and more appealing than the base R biplot() function.

Usage

ggplot_pca(
  x,
  choices = 1:2,
  scale = 1,
  pc.biplot = TRUE,
  labels = NULL,
  labels_textsize = 3,
  labels_text_placement = 1.5,
  groups = NULL,
  ellipse = TRUE,
  ellipse_prob = 0.68,
  ellipse_size = 0.5,
  ellipse_alpha = 0.5,
  points_size = 2,
  points_alpha = 0.25,
  arrows = TRUE,
  arrows_colour = "darkblue",
  arrows_size = 0.5,
  arrows_textsize = 3,
  arrows_textangled = TRUE,
  arrows_alpha = 0.75,
  base_textsize = 10,
  ...
)

Source

The ggplot_pca() function is based on the ggbiplot() function from the ggbiplot package by Vince Vu, as found on GitHub: https://github.com/vqv/ggbiplot (retrieved: 2 March 2020, their latest commit: 7325e88; 12 February 2015).

As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:

  1. Rewritten code to remove the dependency on packages plyr, scales and grid

  2. Parametrised more options, like arrow and ellipse settings

  3. Hardened all input possibilities by defining the exact type of user input for every argument

  4. Added total amount of explained variance as a caption in the plot

  5. Cleaned all syntax based on the lintr package, fixed grammatical errors and added integrity checks

  6. Updated documentation

Arguments

x

an object returned by pca(), prcomp() or princomp()

choices

length 2 vector specifying the components to plot. Only the default is a biplot in the strict sense.

scale

The variables are scaled by lambda ^ scale and the observations are scaled by lambda ^ (1-scale) where lambda are the singular values as computed by princomp. Normally 0 <= scale <= 1, and a warning will be issued if the specified scale is outside this range.

pc.biplot

If true, use what Gabriel (1971) refers to as a "principal component biplot", with lambda = 1 and observations scaled up by sqrt(n) and variables scaled down by sqrt(n). Then inner products between variables approximate covariances and distances between observations approximate Mahalanobis distance.

labels

an optional vector of labels for the observations. If set, the labels will be placed below their respective points. When using the pca() function as input for x, this will be determined automatically based on the attribute non_numeric_cols, see pca().

labels_textsize

the size of the text used for the labels

labels_text_placement

adjustment factor the placement of the variable names (>=1 means further away from the arrow head)

groups

an optional vector of groups for the labels, with the same length as labels. If set, the points and labels will be coloured according to these groups. When using the pca() function as input for x, this will be determined automatically based on the attribute non_numeric_cols, see pca().

ellipse

a logical to indicate whether a normal data ellipse should be drawn for each group (set with groups)

ellipse_prob

statistical size of the ellipse in normal probability

ellipse_size

the size of the ellipse line

ellipse_alpha

the alpha (transparency) of the ellipse line

points_size

the size of the points

points_alpha

the alpha (transparency) of the points

arrows

a logical to indicate whether arrows should be drawn

arrows_colour

the colour of the arrow and their text

arrows_size

the size (thickness) of the arrow lines

arrows_textsize

the size of the text at the end of the arrows

arrows_textangled

a logical whether the text at the end of the arrows should be angled

arrows_alpha

the alpha (transparency) of the arrows and their text

base_textsize

the text size for all plot elements except the labels and arrows

...

arguments passed on to functions

Details

The colours for labels and points can be changed by adding another scale layer for colour, such as scale_colour_viridis_d() and scale_colour_brewer().

Examples

# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.

# \donttest{
if (require("dplyr")) {
  # calculate the resistance per group first
  resistance_data <- example_isolates %>%
    group_by(
      order = mo_order(mo), # group on anything, like order
      genus = mo_genus(mo)
    ) %>% #   and genus as we do here;
    filter(n() >= 30) %>% # filter on only 30 results per group
    summarise_if(is.rsi, resistance) # then get resistance of all drugs

  # now conduct PCA for certain antimicrobial drugs
  pca_result <- resistance_data %>%
    pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)

  summary(pca_result)

  # old base R plotting method:
  biplot(pca_result)

  # new ggplot2 plotting method using this package:
  if (require("ggplot2")) {
    ggplot_pca(pca_result)

    # still extendible with any ggplot2 function
    ggplot_pca(pca_result) +
      scale_colour_viridis_d() +
      labs(title = "Title here")
  }
}
#> Warning: Introducing NA: only 14 results available for PEN in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for OXA in group: order =
#> "Enterobacterales", genus = "Escherichia" (minimum = 30).
#> Warning: Introducing NA: no results available for OXA in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: no results available for OXA in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: only 13 results available for OXA in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: only 15 results available for OXA in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for OXA in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: no results available for FLC in group: order =
#> "Enterobacterales", genus = "Escherichia" (minimum = 30).
#> Warning: Introducing NA: no results available for FLC in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: no results available for FLC in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: only 13 results available for FLC in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for FLC in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: only 26 results available for AMX in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: only 26 results available for AMP in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: only 27 results available for TZP in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: only 12 results available for CZO in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: only 5 results available for CZO in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: only 27 results available for FEP in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: only 23 results available for FEP in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: only 29 results available for FOX in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: only 26 results available for AMK in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: only 6 results available for AMK in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: only 17 results available for AMK in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: no results available for KAN in group: order =
#> "Enterobacterales", genus = "Escherichia" (minimum = 30).
#> Warning: Introducing NA: no results available for KAN in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: no results available for KAN in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: only 6 results available for NIT in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: only 17 results available for NIT in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: only 8 results available for FOS in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: only 2 results available for FOS in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: no results available for FOS in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for FOS in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for FOS in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: only 7 results available for LNZ in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: only 5 results available for CIP in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: only 23 results available for CIP in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: only 2 results available for MFX in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: only 2 results available for MFX in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: no results available for MFX in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: only 7 results available for MFX in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for MFX in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: only 6 results available for TEC in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: only 3 results available for TCY in group: order =
#> "Enterobacterales", genus = "Escherichia" (minimum = 30).
#> Warning: Introducing NA: only 2 results available for TCY in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: only 18 results available for TGC in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: only 7 results available for TGC in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for DOX in group: order =
#> "Enterobacterales", genus = "Escherichia" (minimum = 30).
#> Warning: Introducing NA: no results available for DOX in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: only 2 results available for DOX in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: only 27 results available for IPM in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: only 25 results available for MEM in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: only 26 results available for MEM in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: no results available for MTR in group: order =
#> "Caryophanales", genus = "Staphylococcus" (minimum = 30).
#> Warning: Introducing NA: only 2 results available for MTR in group: order =
#> "Enterobacterales", genus = "Escherichia" (minimum = 30).
#> Warning: Introducing NA: no results available for MTR in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: no results available for MTR in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: no results available for MTR in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for MTR in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for MTR in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: no results available for CHL in group: order =
#> "Enterobacterales", genus = "Escherichia" (minimum = 30).
#> Warning: Introducing NA: no results available for CHL in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: no results available for CHL in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: no results available for CHL in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for CHL in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: only 9 results available for COL in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: no results available for MUP in group: order =
#> "Enterobacterales", genus = "Escherichia" (minimum = 30).
#> Warning: Introducing NA: no results available for MUP in group: order =
#> "Enterobacterales", genus = "Klebsiella" (minimum = 30).
#> Warning: Introducing NA: no results available for MUP in group: order =
#> "Enterobacterales", genus = "Proteus" (minimum = 30).
#> Warning: Introducing NA: no results available for MUP in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for MUP in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for MUP in group: order =
#> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).
#> Warning: Introducing NA: no results available for RIF in group: order =
#> "Lactobacillales", genus = "Enterococcus" (minimum = 30).
#> Warning: Introducing NA: no results available for RIF in group: order =
#> "Lactobacillales", genus = "Streptococcus" (minimum = 30).
#> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"
#>   and "TOB". Total observations available: 7.
#> Groups (n=4, named as 'order'):
#> [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales" 
#> 


# }