factorMap: Plot an MFA factor map for individuals or partial factor map...

In andreamrau/padma: Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Plot an MFA factor map for individuals or partial factor map based on padma analysis

Description

Produce an MFA factor map for individuals, or MFA partial factor map for a given individual, for a pair of dimensions provided by the user.

Usage

factorMap(
  padma_obj,
  partial_id = NULL,
  dim_x = 1,
  dim_y = 2,
  plot_ellipse = TRUE,
  ggplot = TRUE,
  repel_labels = ifelse(ggplot == TRUE, TRUE, FALSE)
)

Arguments

padma_obj	Output from running the padma function (with 'full_results = TRUE')
partial_id	Index or sample name to be plotted for a partial factor map.
dim_x	Dimension number of the MFA to be plotted on the x-axis.
dim_y	Dimension number of the MFA to be plotted on the y-axis.
plot_ellipse	If TRUE, superimpose a normal confidence ellipsis on the factor map.
ggplot	If TRUE, use ggplot2 for plotting
repel_labels	If TRUE, use ggrepel to repel sample labels from each other

Value

Plot, or factor map of class ggplot if ggplot2 = TRUE.

Examples

LUAD_subset <- padma::LUAD_subset
## Create MultiAssayExperiment object with LUAD data
omics_data <- 
  list(rnaseq = as.matrix(LUAD_subset$rnaseq),
       methyl = as.matrix(LUAD_subset$methyl),
       mirna = as.matrix(LUAD_subset$mirna),
       cna = as.matrix(LUAD_subset$cna))
pheno_data <- 
  data.frame(LUAD_subset$clinical, 
             row.names = LUAD_subset$clinical$bcr_patient_barcode)
mae <-
  suppressMessages(
    MultiAssayExperiment::MultiAssayExperiment(
      experiments = omics_data, colData = pheno_data))

## Run padma
run_padma <- 
  padma(mae, gene_map = padma::mirtarbase,
        pathway_name = "c2_cp_BIOCARTA_D4GDI_PATHWAY", verbose = FALSE)

summary(run_padma)

## padma plots
## Not run: 
factorMap(run_padma, dim_x = 1, dim_y = 2)
factorMap(run_padma, dim_x = 1, dim_y = 2,
           partial_id = "TCGA-78-7536")
omicsContrib(run_padma, max_dim = 10)

## End(Not run)

andreamrau/padma documentation built on Oct. 8, 2022, 9 a.m.