pca_plot: pca_plot

In eonurk/cinaR: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

pca_plot

Description

pca_plot

Usage

pca_plot(results, overlaid.info, sample.names = NULL, show.names = TRUE)

Arguments

results	cinaR result object
overlaid.info	overlaid information onto the samples
sample.names	names of the samples shown on pca plot
show.names	logical, if set FALSE sample names will be hidden

Value

ggplot object

Examples

#' library(cinaR)
data(atac_seq_consensus_bm) # calls 'bed'

# creating dummy results
results <- NULL
results[["cp"]] <- bed[,c(4:25)]

# a vector for comparing the examples
contrasts <- sapply(strsplit(colnames(bed), split = "-", fixed = TRUE),
                    function(x){x[1]})[4:25]

## overlays the contrasts info onto PCA plots
pca_plot(results, contrasts)

## you can overlay other information as well,
## as long as it is the same length with the
## number of samples.

sample.info <- c(rep("Group A", 11), rep("Group B", 11))
pca_plot(results, sample.info, show.names = FALSE)

eonurk/cinaR documentation built on May 23, 2024, 7:08 a.m.