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Plot heatmaps using the exposures matrix

Source: R/plot_heatmap.R
plot_heatmap.Rd

The exposures for different signatures can be visualized using a heatmap with this function. Heatmaps make it easier to visualize the data by representing the magnitude of exposure values as color in 2-dimensions. The variation in color intensity can help see if the exposures are clustered or how they vary over space. Exposures can be normalized by providing the proportional argument. Column annotations can also be seen by passing the col_annot argument.

Usage

plot_heatmap(
  musica,
  model_name,
  modality = "SBS96",
  result_name = "result",
  proportional = FALSE,
  show_column_names = FALSE,
  show_row_names = TRUE,
  scale = TRUE,
  subset_tumor = NULL,
  subset_signatures = NULL,
  annotation = NULL,
  ...
)

Arguments

musica

A musica object containing a mutational discovery or prediction.

model_name

The name of the desired model.

modality

The modality of the model. Must be "SBS96", "DBS78", or "IND83". Default "SBS96".

result_name

Name of the result list entry containing desired model. Default "result".

proportional

If TRUE, then the exposures will be normalized to between 0 and 1 by dividing by the total number of counts for each sample. Default FALSE.

show_column_names

Boolean check. If True, column names are shown. Otherwise, they aren't. Default FALSE

show_row_names

Boolean check. If True, row names are shown. Otherwise, they aren't. Default FALSE

scale

Boolean check. If True, values are scaled by z-score. Otherwise, they aren't. Default TRUE

subset_tumor

Users can specify certain tumor types on which they want to subset the exposure matrix for plotting the heatmap.

subset_signatures

Users can specify certain signatures on which they want to subset the exposure matrix plotting the heatmap.

annotation

Users have the option of plotting the exposure matrix based on their given annotation like Tumor_Subtypes or age. Error given if the user given annotation doesn't exist in the res_annot annotation object.

...

Ellipsis used for passing any arguments directly to the ComplexHeatmap's heatmap function.

Value

Generates a heatmap for using the exposure matrix.

Examples

data(res_annot)
plot_heatmap(
  musica = res_annot, model_name = "res_annot",
  proportional = TRUE, scale = TRUE, annotation = "Tumor_Subtypes"
)