complex_heatmap_exposures: Heatmap to cluster the PIDs on their signature exposures...

In slw287r/yapsa: Yet Another Package for Signature Analysis

Description

The PIDs are clustered according to their signature exposures. uses package ComplexHeatmap by Zuguang Gu. This function calls:

• rowAnnotation,

• HeatmapAnnotation and

• Heatmap

Usage

complex_heatmap_exposures(
  in_exposures_df,
  in_subgroups_df,
  in_signatures_ind_df,
  in_data_type = "norm exposures",
  in_method = "manhattan",
  in_subgroup_column = "subgroup",
  in_subgroup_colour_column = NULL,
  in_palette = colorRamp2(c(0, 0.2, 0.4, 0.6), c("white", "yellow", "orange", "red")),
  in_cutoff = 0,
  in_filename = NULL,
  in_column_anno_borders = FALSE,
  in_row_anno_borders = 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_signatures_ind_df	A data frame containing meta information about the signatures, especially the asserted colour
in_data_type	Title in the figure
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_subgroup_colour_column	Indicates the name of the column in which the colour information for subgroups is encoded in in_subgroups_df. If NULL, a rainbow palette is used instead.
in_palette	Palette with colours for the heatmap. Default is colorRamp2(c(0, 0.2, 0.4, 0.6), c('white','yellow','orange','red'))
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 heatmap. If none is specified, the figure will be plotted to the running environment.
in_column_anno_borders	Whether or not to draw separating lines between the fields in the annotation
in_row_anno_borders	Whether or not to draw separating lines between the fields in the annotation

Details

It might be necessary to install the newest version of the development branch of the packages circlize and ComplexHeatmap by Zuguang Gu: devtools::install_github("jokergoo/circlize") and devtools::install_github("jokergoo/ComplexHeatmap")

Value

The function doesn't return any value.

See Also

Heatmap

Examples

 data(lymphoma_cohort_LCD_results)
 complex_heatmap_exposures(
   rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df,
   COSMIC_subgroups_df,
   chosen_signatures_indices_df,
   in_data_type="norm exposures",
   in_subgroup_colour_column="col",
   in_method="manhattan",
   in_subgroup_column="subgroup")

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