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

View source: R/plot_functions.R

factorMapR Documentation

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 June 15, 2024, 8:39 a.m.