annotation_exposures_list_barplot: Plot the exposures of a cohort with different layers of...

Description Usage Arguments Details Value See Also Examples

View source: R/plot_functions.R

Description

The exposures H, determined by NMF or by LCD, are displayed as a stacked barplot by calling Heatmap. The x-axis displays the PIDs (patient identifier or sample), the y-axis the counts attributed to the different signatures with their respective colours per PID. It is analogous to plot_exposures. As many layers of information as desired can be added via an annotation data frame. The annotation data is handled in a way similar to annotation_heatmap_exposures. In comparison to annotation_exposures_barplot allows this function to deal with a list of differn signature and mutation types. This function calls:

Usage

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annotation_exposures_list_barplot(
  in_exposures_list,
  in_signatures_ind_list,
  in_subgroups_list,
  in_annotation_list,
  ylab = NULL,
  title = "",
  in_indel_sigs = FALSE,
  in_labels = FALSE,
  in_barplot_borders = TRUE,
  in_column_anno_borders = FALSE,
  in_annotation_legend_side = "right",
  in_padding = unit(c(2, 20, 2, 2), "mm"),
  in_annotation = NULL
)

Arguments

in_exposures_list

A list of numerical data frame encoding the exposures H of different signature types, i.e. which signature contributes how much to which PID (patient identifier or sample).

in_signatures_ind_list

A list of data frame containing meta information about the each signature type individually

in_subgroups_list

A list of data frame indicating of each siganture type which PID (patient or sample identifyier) belongs to which subgroup

in_annotation_list

A list data frame indicating which PID (patient or sample identifyier) belongs to which subgroup for all layers of annotation and a list indicating colour attributions for all layers of annotation for each siganture type individually

ylab

String indicating the column name in in_subgroups_df to take the subgroup information from.

title

Title for the plot to be created.

in_indel_sigs

Tag which is default FALSE when whole genome data are analysed the tag will be TRUE

in_labels

Whether or not to show the names of the samples.

in_barplot_borders

Whether or not to show border lines in barplot

in_column_anno_borders

Whether or not to draw separating lines between the fields in the annotation

in_annotation_legend_side

Where to put the legends of the annotation df, default is right.

in_padding

Parameter passed on to function draw

in_annotation

A full annotation object may also be provided by the educated user.

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")

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

HeatmapAnnotation

Heatmap

decorate_heatmap_body

annotation_heatmap_exposures

plot_exposures

Examples

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YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.