OlinkAnalyze (version 5.1.0)

olink_heatmap_plot: Function to plot a heatmap of the NPX data

Description

Generates a heatmap using pheatmap::pheatmap of all samples from NPX data.

Usage

olink_heatmap_plot(
  df,
  check_log = NULL,
  variable_row_list = NULL,
  variable_col_list = NULL,
  center_scale = TRUE,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  show_rownames = TRUE,
  show_colnames = TRUE,
  colnames = "both",
  annotation_legend = TRUE,
  fontsize = 10,
  na_col = "black",
  ...
)

Value

An object of class ggplot, generated from the gtable

returned by pheatmap::pheatmap.

Arguments

df

Data frame in long format with SampleID, NPX, OlinkID, Assay and columns of choice for annotations.

check_log

output from check_npx on df

variable_row_list

Columns in df to be annotated for rows in the heatmap.

variable_col_list

Columns in df to be annotated for columns in the heatmap.

center_scale

Logical. If data should be centered and scaled across assays (default TRUE).

cluster_rows

Logical. Determining if rows should be clustered (default TRUE).

cluster_cols

Logical. Determining if columns should be clustered (default TRUE).

show_rownames

Logical. Determining if row names are shown (default TRUE).

show_colnames

Logical. Determining if column names are shown (default TRUE).

colnames

Character. Determines how to label the columns. Must be 'assay', 'oid', or 'both' (default 'both').

annotation_legend

Logical. Determining if legend for annotations should be shown (default TRUE).

fontsize

Fontsize (default 10)

na_col

Color of cells with NA (default black)

...

Additional arguments used in pheatmap::pheatmap

Details

The values are by default scaled across and centered in the heatmap. Columns and rows are by default sorted by by dendrogram. Unique sample names are required.

Examples

# \donttest{
if (rlang::is_installed(pkg = c("ggplotify", "pheatmap"))) {
  npx_data <- npx_data1 |>
    dplyr::filter(
      !stringr::str_detect(
        string = .data[["SampleID"]],
        pattern = "CONT"
      )
    )

  # Heatmap
  OlinkAnalyze::olink_heatmap_plot(
    df = npx_data
  )

  # Heatmap with annotation
  OlinkAnalyze::olink_heatmap_plot(
    df = npx_data,
    variable_row_list = c("Time", "Site")
  )

  # Heatmap with calls from pheatmap
  OlinkAnalyze::olink_heatmap_plot(
    df = npx_data,
    cutree_rows = 3L
  )
}
# }