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Plots sample scores as a scatterplot

Source: R/output_plot.R
plot_samples_score_pair.Rd

Plots the samples score from a pair of latent dimensions from a dimension reduction analysis as a scatterplot.

Usage

plot_samples_score_pair(
  method_output,
  latent_dimensions,
  mo_data = NULL,
  colour_by = NULL,
  shape_by = NULL
)

Arguments

method_output

A single Integration method output generated via the get_output() function, or a list of two integration method outputs.

latent_dimensions

Character vector of length 2 (if method_output is a single output object), or named list of length 2 (if method_output is a list of two output objects). In the first case, gives the name of the two latent dimensions that should be represented. In the second case, the names of the list should correspond to the names of the methods, and the values should each be a character giving for the corresponding method the name of the latent dimension to display.

mo_data

A MultiDataSet object (will be used to extract samples information).

colour_by

Character, name of column in one of the samples metadata tables from mo_data to use for colouring samples in the plot. Default value is NULL.

shape_by

Character, name of column in one of the samples metadata tables from mo_data to use a shape for the samples in the plot. Default value is NULL.

Value

A ggplot.

Examples

if (FALSE) { # \dontrun{
## Let diablo_res be the output from a DIABLO analysis, and mofa_res the
## output from a MOFA analysis. Let mo_set be the corresponding MultiDataSet object.
output_diablo <- get_output_diablo(diablo_res)
output_mofa <- get_output_mofa2(mofa_res)

## Scatterplot of the first two DIABLO components
plot_samples_score_pair(output_diablo, c("Component 1", "Component 2"))

## Adding samples information to the plot - here 'Time' and 'Treatment' should
## two columns in the samples metadata of one of the datasets in mo_set
plot_samples_score_pair(
  output_diablo,
  c("Component 1", "Component 2"),
  mo_data <- mo_set,
  colour_by = "Time",
  shape_by = "Treatment"
)

## Comparing the first MOFA factor to the first DIABLO component
plot_samples_score_pair(
  list(output_diablo, output_mofa),
  list("DIABLO" = "Component 1", "MOFA" = "Factor 1"),
  mo_data <- mo_set,
  colour_by = "Time",
  shape_by = "Treatment"
)

## Giving custom names to the methods
plot_samples_score_pair(
  list("DIABLO prefiltered" = output_diablo, "MOFA full" = output_mofa),
  list("DIABLO prefiltered" = "Component 1", "MOFA full" = "Factor 1")
)
} # }