Plot MDS — plot_mds • NanoMethViz

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

Usage

plot_mds(
  x,
  top = 500,
  plot_dims = c(1, 2),
  labels = colnames(x),
  groups = NULL,
  legend_name = "group"
)

Arguments

x: the log-methylation-ratio matrix.
top: the number of top genes used to calculate pairwise distances.
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. Colour palette can be adjusted using scale_colour_*() functions from ggplot2. If groups is numeric, the points will be coloured by a continuous colour palette. By default, groups is NULL and the points will not be coloured.
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 11:03:08] creating intermediate files...
#> [2025-05-04 11:03:08] parsing chr11...
#> [2025-05-04 11:03:08] parsing chr12...
#> [2025-05-04 11:03:08] parsing chr18...
#> [2025-05-04 11:03:08] parsing chr5...
#> [2025-05-04 11:03:08] parsing chr7...
#> [2025-05-04 11:03:08] parsing chrX...
#> [2025-05-04 11:03:08] 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 11:03:08] creating bsseq object...
#> [2025-05-04 11:03:08] reading in parsed data...
#> [2025-05-04 11:03:08] constructing matrices...
#> [2025-05-04 11:03:09] done
lmr <- bsseq_to_log_methy_ratio(bss)
plot_mds(lmr)