hclust_exposures: Cluster the PIDs according to their signature exposures

In slw287r/yapsa: Yet Another Package for Signature Analysis

Description

The PIDs are clustered according to their signature exposures by calling first creating a distance matrix:

• dist, then

• hclust and then

• labels_colors to colour the labels (the text) of the leaves in the dendrogram.

Typically one colour per subgroup.

Usage

hclust_exposures(
  in_exposures_df,
  in_subgroups_df,
  in_method = "manhattan",
  in_subgroup_column = "subgroup",
  in_palette = NULL,
  in_cutoff = 0,
  in_filename = NULL,
  in_shift_factor = 0.3,
  in_cex = 0.2,
  in_title = "",
  in_plot_flag = FALSE
)

Arguments

in_exposures_df	Numerical data frame encoding the exposures H, i.e. which signature contributes how much to which PID (patient identifier or sample).
in_subgroups_df	A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup
in_method	Method of the clustering to be supplied to dist. Can be either of: euclidean, maximum, manhattan, canberra, binary or minkowski
in_subgroup_column	Indicates the name of the column in which the subgroup information is encoded in in_subgroups_df
in_palette	Palette with colours or colour codes for the labels (the text) of the leaves in the dendrogram. Typically one colour per subgroup. If none is specified, a rainbow palette of the length of the number of subgroups will be used as default.
in_cutoff	A numeric value less than 1. Signatures from within W with an overall exposure less than in_cutoff will be discarded for the clustering.
in_filename	A path to save the dendrogram. If none is specified, the figure will be plotted to the running environment.
in_shift_factor	Graphical parameter to adjust figure to be created
in_cex	Graphical parameter to adjust figure to be created
in_title	Title in the figure to be created under in_filename
in_plot_flag	Whether or not to display the dendrogram

Value

A list with entries hclust and dendrogram.

• hclust: The object created by hclust

• dendrogram: The above object wrapped in as.dendrogram

See Also

hclust

dist

labels_colors

Examples

 data(lymphoma_cohort_LCD_results)
 hclust_exposures(rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df,
                  COSMIC_subgroups_df,
                  in_method="manhattan",
                  in_subgroup_column="subgroup")

slw287r/yapsa documentation built on June 7, 2020, 12:46 a.m.