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

Description Usage Arguments Details Value See Also Examples

View source: R/plot_functions.R

Description

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:

Usage

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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"
)

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_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.

Details

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")

Value

The function doesn't return any value.

See Also

Heatmap

complex_heatmap_exposures

Examples

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