Heatmap summary of missing values — hd_na

hd_na_search() provides a visual summary of missing values in a dataset as an annotated heatmap. It allows the user to specify the metadata columns to include in the summary and the color palette to use for the heatmap annotations.

Usage

hd_na_search(
  dat,
  metadata = NULL,
  annotation_vars = NULL,
  palette = NULL,
  x_labels = FALSE,
  y_labels = FALSE
)

Arguments

dat: An HDAnalyzeR object or a dataset in wide format and sample ID as its first column.
metadata: A dataset containing the metadata information with the sample ID as the first column. If a HDAnalyzeR object is provided, this parameter is not needed.
annotation_vars: The metadata columns to include in the summary.
palette: A list of color palettes for the heatmap annotations. The names of the list should match the column names in annotation_vars. Default is NULL.
x_labels: If TRUE, show x-axis labels. Default is FALSE.
y_labels: If TRUE, show y-axis labels. Default is FALSE.

Value

A list containing the summary of missing values and the heatmap visualization.

Details

When using continuous metadata variables, they are automatically binned into categories of 5 bins to make the heatmap more informative and easier to interpret. If the user wants to use a different number of bins, they can bin the data before using the hd_bin_columns() function and its bins argument.

Also, when coloring annotations, the user can use custom palettes or the Human Protein Atlas (HPA) palettes. It is not required to provide a palette for all annotations, but when a palette is provided, it must be in correct format (check examples bellow).

Examples

# Create the HDAnalyzeR object providing the data and metadata
hd_object <- hd_initialize(example_data, example_metadata)

# Use custom palettes for coloring annotations
palette = list(Sex = c(M = "blue", F = "pink"))
na_res <- hd_na_search(hd_object,
                       annotation_vars = c("Age", "Sex"),
                       palette = palette)
na_res$na_heatmap


# Use a mix of custom and HPA palettes for coloring annotations
palette = list(Disease = "cancers12", Sex = c(M = "blue", F = "pink"))
na_res <- hd_na_search(hd_object,
                       annotation_vars = c("Disease", "Sex"),
                       palette = palette)
na_res$na_heatmap