complex_heatmap_exposures: Heatmap to cluster the PIDs on their signature exposures...
In eilslabs/YAPSA: Yet Another Package for Signature Analysis

Description Usage Arguments Details Value See Also Examples

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

rowAnnotation,
HeatmapAnnotation and
Heatmap

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)

`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

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")

The function doesn't return any value.

Heatmap

 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")