overview_heatmap: A overview of NPX value in heatmap

In ge11232002/OlinkR: A toolkit for Olink data analysis

Description

Plot the NPX value in a heatmap to spot any potential clustering and outliers

Usage

overview_heatmap(
  se,
  scale = c("none", "row", "column"),
  cluster_samples = FALSE,
  cluster_features = FALSE,
  ...
)

Arguments

se	A SummarizedExperiment object.
scale	character(1): how to scale (z-score) the data. "none": no scaling. "sample": scale across the samples. "feature": scale across the features (proteins).
cluster_samples	logical(1): do the samples clustering.
cluster_features	logical(1): do the samples clustering.
...	graphical parameter passed to pheatmap.

Value

A pheatmap object.

Author(s)

Ge Tan

Examples

npxFn <- system.file("extdata",
                     c("20200507_Inflammation_NPX_1.xlsx",
                       "20200625_Inflammation_NPX_2.xlsx"),
                     package = "OlinkR")
metaFn <- system.file("extdata", "Inflammation_Metadata.xlsx", package = "OlinkR")
se <- as_se(read_npx(npxFn, metaFn))
overview_heatmap(se)

ge11232002/OlinkR documentation built on Jan. 17, 2022, 8:28 p.m.