MS Metabolomics Data Processing Utilities

Description Usage Arguments Value See Also Examples

Visualize an overlay of a score plot and a loading plot using the poplin_reduce output.

## Default S3 method:
poplin_biplot(
  x,
  y,
  comp = c(1, 2),
  group,
  group_col = NULL,
  point_size = 1.5,
  point_shape_by_group = FALSE,
  label = FALSE,
  label_size = 3.88,
  label_subset = NULL,
  ellipse = FALSE,
  xlab = NULL,
  ylab = NULL,
  title = NULL,
  legend = TRUE,
  arrow_len = 0.2,
  arrow_col = "red",
  arrow_alpha = 0.3,
  arrow_label = TRUE,
  arrow_label_ext = 1.1,
  arrow_label_size = 3.88,
  arrow_label_col = "red",
  arrow_label_subset = NULL,
  ...
)

## S3 method for class 'poplin.pca'
poplin_biplot(x, comp = c(1, 2), group, label = FALSE, ...)

## S3 method for class 'poplin.plsda'
poplin_biplot(
  x,
  comp = c(1, 2),
  group = attr(x, "Y.observed"),
  label = label,
  ...
)

## S3 method for class 'poplin'
poplin_biplot(x, xin, comp = c(1, 2), group, label = FALSE, ...)

`x`	A dimension-reduced data matrix produced by poplin_reduce or poplin object containing dimension-reduced data.
`y`	A data matrix for loadings. Not required for the reduce_pca and reduce_plsda outputs.
`comp`	A numeric vector of length 2 indicating two components to plot.
`group`	A discrete variable to visualize the grouping structure.
`group_col`	A vector of colors with the same length of unique values in `group`.
`point_size`	Numeric controlling the size of points.
`point_shape_by_group`	Logical controlling whether each group have different shapes of data points. Also can be a numeric vector with the same length of unique values in `group` to manually set point shapes.
`label`	Logical controlling whether score labels are shown instead of points.
`label_size`	Numeric controlling the size of labels.
`label_subset`	A character vector specifying a subset of score labels to display.
`ellipse`	Logical controlling whether data ellipses are shown using the stat_ellipse (ggplot2 package).
`xlab`	The title of x-axis of the plot.
`ylab`	The title of y-axis of the plot.
`title`	The main title of the plot.
`legend`	Logical controlling whether the plot legend is shown.
`arrow_len`	Numeric controlling the length of arrow head.
`arrow_col`	Character indicating the color of arrows.
`arrow_alpha`	Numeric controlling the transparency of arrow.
`arrow_label`	Logical controlling whether text labels for arrows are shown.
`arrow_label_ext`	Numeric controlling the scalar extension for arrow labels.
`arrow_label_size`	Numeric value controlling the size of arrow labels.
`arrow_label_col`	Character indicating the color of arrow labels. labels.
`arrow_label_subset`	A character vector specifying a subset of arrow labels to display.
`...`	Arguments passed to the default method.
`xin`	Character specifying the name of data to retrieve from `x` when `x` is a poplin object

A ggplot object.

poplin_reduce, poplin_scoreplot.

data(faahko_poplin)

## sample group variable
group <- colData(faahko_poplin)$sample_group

## poplin object
poplin_biplot(faahko_poplin, xin = "pca", group = group)

## matrix
m <- poplin_reduced(faahko_poplin, "pca")
poplin_biplot(m, group = group, arrow_col = "orange",
              arrow_label_subset = rownames(faahko_poplin)[seq_len(10)])