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Plots omics data as heatmap

Source: R/multidataset_plots.R
plot_data_heatmap.Rd

For a given set of features, plots their value across the samples as a heatmap.

Usage

plot_data_heatmap(
  mo_data,
  features,
  center = FALSE,
  scale = FALSE,
  samples = NULL,
  only_common_samples = FALSE,
  samples_info = NULL,
  features_info = NULL,
  colours_list = NULL,
  label_cols = NULL,
  truncate = NULL,
  legend_title_size = 10,
  legend_text_size = 10,
  legend_ncol = 1,
  ...
)

Arguments

mo_data

A MultiDataSet::MultiDataSet object.

features

Character vector, the ID of features to show in the plot.

center

Logical, whether the data should be centered (feature-wise). Default value is FALSE.

scale

Logical, whether the data should be scaled (feature-wise). Default value is FALSE.

samples

Character vector, the ID of samples to include in the plot. If NULL (default), all samples will be used.

only_common_samples

Logical, whether only samples that are present in all datasets should be plotted. Default value is FALSE.

samples_info

Character vector, column names from the samples metadata tables of the datasets to be represented in the plot as samples annotation.

features_info

Named list of character vectors, where each element corresponds to a dataset, and gives the column names from the features metadata of the dataset to be represented in the plot as features annotation. The names of the list must correspond to dataset names in the mo_data object.

colours_list

Named list, where each element gives the colour palette to use in the samples or features annotation. Names must match values in samples_info vector and elements of features_info list. For continuous palettes, must use circlize::colorRamp2() function (see the ComplexHeatmap reference book).

label_cols

Character or named list of character, giving for each dataset the name of the column in the corresponding features metadata to use as label. If one value, will be used for all datasets. If list, the names must correspond to the names of the datasets in mo_data. If a dataset is missing from the list or no value is provided, feature IDs will be used as labels. Alternatively, use feature_id to get the feature IDs as labels.

truncate

Integer, width to which the labels should be truncated (to avoid issues with very long labels in plots). If NULL (default value), no truncation will be performed.

legend_title_size

Integer, size in points of legend title.

legend_text_size

Integer, size in points of legend elements text.

legend_ncol

Integer, number of columns in the legend. Default value is 1.

...

Additional arguments passed to the ComplexHeatmap::Heatmap() function.

Value

A ComplexHeatmap::Heatmap object.

Examples

if (FALSE) { # \dontrun{
## Selecting at random 3 features from each dataset
random_features <- get_features(mo_set) |>
  map(sample, size = 3, replace = FALSE) |>
  unlist() |>
  unname()

plot_data_heatmap(
  mo_set,
  random_features,
  center = TRUE,
  scale = TRUE,
  show_column_names = FALSE,
  only_common_samples = TRUE,
  samples_info = c("status", "day_on_feed"),
  features_info = c("chromosome"),
  colours_list = list(
    "status" = c("Control" = "gold", "BRD" = "navyblue"),
    "day_on_feed" = colorRamp2(c(5, 65), c("white", "pink3"))
  ),
  label_cols = list(
     "rnaseq" = "Name",
    "metabolome" = "name"
  )
 )
} # }