complex_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. uses package ComplexHeatmap by Zuguang Gu. This function calls:

Usage

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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

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 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.