MOFA (version 1.3.1)

plotFactorScatter: Scatterplot of two latent factors

Description

Scatterplot of the values of two latent factors.

Usage

plotFactorScatter(object, factors, color_by = NULL, shape_by = NULL,
  name_color = "", name_shape = "", dot_size = 1.5, dot_alpha = 1,
  showMissing = TRUE)

Arguments

object

a trained MOFAmodel object.

factors

a vector of length two with the factors to plot. Factors can be specified either as a characters using the factor names, or as numeric with the index of the factors

color_by

specifies groups or values used to color the samples. This can be either a character giving the name of a feature present in the training data, a character giving the same of a covariate (only if using MultiAssayExperiment as input), or a vector of the same length as the number of samples specifying discrete groups or continuous numeric values.

shape_by

specifies groups or values used to shape the samples. This can be either a character giving the name of a feature present in the training data, a character giving the same of a covariate (only if using MultiAssayExperiment as input), or a vector of the same length as the number of samples specifying discrete groups.

name_color

name for color legend.

name_shape

name for shape legend.

dot_size

dot size (default is 1.5).

dot_alpha

dot transparency (default is 1.0, no transparency).

showMissing

logical indicating whether to include samples for which shape_by or color_by is missing.

Value

Returns a ggplot2 object

Details

One of the first steps for the annotation of factors is to visualise and group/color them using known covariates such as phenotypic or clinical data. This method generates a single scatterplot for the combination of two latent factors. Similar functions are plotFactorScatters for doing multiple scatter plots and plotFactorBeeswarm for doing Beeswarm plots for single factors.

Examples

# NOT RUN {
# Example on the CLL data
filepath <- system.file("extdata", "CLL_model.hdf5", package = "MOFAdata")
MOFA_CLL <- loadModel(filepath)
plotFactorScatter(MOFA_CLL, factors=1:2)
plotFactorScatter(MOFA_CLL, factors=1:2, color_by= "IGHV", shape_by="trisomy12", showMissing=FALSE)

# Example on the scMT data
filepath <- system.file("extdata", "scMT_model.hdf5", package = "MOFAdata")
MOFA_scMT <- loadModel(filepath)
plotFactorScatter(MOFA_scMT, factors=c(1,3))
# }