annotation_heatmap_exposures: Heatmap to cluster the PIDs on their signature exposures...
In slw287r/yapsa: Yet Another Package for Signature Analysis

Description Usage Arguments Details Value See Also Examples

The PIDs are clustered according to their signature exposures. The procedure is analogous to complex_heatmap_exposures, but enabling more than one annotation row for the PIDs. This function calls:

rowAnnotation,
HeatmapAnnotation and
Heatmap

annotation_heatmap_exposures(
  in_exposures_df,
  in_annotation_df,
  in_annotation_col,
  in_signatures_ind_df,
  in_data_type = "norm exposures",
  in_method = "manhattan",
  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_show_PIDs = TRUE,
  in_annotation_legend_side = "right"
)

`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_annotation_df`	A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup for all layers of annotation
`in_annotation_col`	A list indicating colour attributions for all layers of annotation
`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_palette`	Palette with colours or colour codes 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
`in_show_PIDs`	Whether or not to show the PIDs on the x-axis
`in_annotation_legend_side`	Where to put the legends of the annotation df, default is right.

One additional parameter, in_show_legend_bool_vector, indicating which legends to display, is planned but deactivated in this version of the package. In order to use this features, it will be necessary to install the newest version 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

complex_heatmap_exposures