Plot PCA

Plot multi-dimensional scaling plot using algorithm of BiocSingular::runPCA(). It is recommended this be done with the log-methylation-ratio matrix generated by bsseq_to_log_methy_ratio().

Usage

plot_pca(
  x,
  plot_dims = c(1, 2),
  labels = colnames(x),
  groups = NULL,
  legend_name = "group"
)

Arguments

x

the log-methylation-ratio matrix.

plot_dims

the numeric vector of the two dimensions to be plotted.

labels

the character vector of labels for data points. By default uses column names of x, set to NULL to plot points.

groups

the character vector of groups the data points will be coloured by.

legend_name

the name for the legend.

Value

ggplot object of the MDS plot.

Examples

nmr <- load_example_nanomethresult()
bss <- methy_to_bsseq(nmr)
#> [2025-05-04 11:03:09] creating intermediate files...
#> [2025-05-04 11:03:09] parsing chr11...
#> [2025-05-04 11:03:09] parsing chr12...
#> [2025-05-04 11:03:09] parsing chr18...
#> [2025-05-04 11:03:09] parsing chr5...
#> [2025-05-04 11:03:09] parsing chr7...
#> [2025-05-04 11:03:09] parsing chrX...
#> [2025-05-04 11:03:09] samples found: B6Cast_Prom_3_cast B6Cast_Prom_3_bl6 B6Cast_Prom_2_cast B6Cast_Prom_2_bl6 B6Cast_Prom_1_cast B6Cast_Prom_1_bl6 
#> [2025-05-04 11:03:09] creating bsseq object...
#> [2025-05-04 11:03:09] reading in parsed data...
#> [2025-05-04 11:03:09] constructing matrices...
#> [2025-05-04 11:03:10] done
lmr <- bsseq_to_log_methy_ratio(bss)
plot_pca(lmr)