factorMap {padma} | R 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 = LUAD_subset$rnaseq,
           methyl = LUAD_subset$methyl,
           mirna = LUAD_subset$mirna,
           cna = LUAD_subset$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
    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)

[Package padma version 1.0.0 Index]