View source: R/plot_functions.R
factorMap | R Documentation |
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.
factorMap(
padma_obj,
partial_id = NULL,
dim_x = 1,
dim_y = 2,
plot_ellipse = TRUE,
ggplot = TRUE,
repel_labels = ifelse(ggplot == TRUE, TRUE, FALSE)
)
padma_obj |
Output from running the |
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 |
ggplot |
If |
repel_labels |
If |
Plot, or factor map of class ggplot
if ggplot2 = TRUE
.
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.