Package 'express'

List Available Datasets

Description

This function lists all available datasets for use with the express package. It reads a predefined TSV file containing dataset information and returns it as a data frame.

Usage

express_available_datasets(url = FALSE)

Arguments

url	show the URL from which the data will be pulled

Value

A data frame containing the available datasets. The data frame includes columns such as name, type, url, and description.

Examples

# List all available datasets
datasets <- express_available_datasets()
print(datasets)

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Fetch and Plot Precomputed Dataset

Description

This function retrieves and visualizes precomputed t-SNE data from a specified dataset. It fetches the data from a URL associated with the dataset name provided, and then either returns the data directly or creates a ggplot2 visualization of the t-SNE dimensions.

Usage

express_precomputed(
  dataset,
  datatype = c("expression", "methylation"),
  interactive = FALSE,
  just_return_data = FALSE,
  title = "auto",
  show_axis_titles = FALSE
)

Arguments

dataset	A string specifying the name of the dataset to be retrieved. The dataset must be one of the available datasets listed by express_available_datasets().
datatype	A string indicating whether to retrieve expression or methylation data
interactive	A logical value indicating whether the plot should be interactive. Currently, this parameter is not used in the function.
just_return_data	A logical value indicating whether to return only the dataset without generating a plot. Defaults to FALSE.
show_axis_titles	A boolean indicating whether to show axis titles

Value

If just_return_data is TRUE, a data.table containing the dataset is returned. If just_return_data is FALSE and the dataset type is "tsne", a ggplot2 object representing the t-SNE plot is returned. If the dataset type is not "tsne", an error is raised.

Examples

# Retrieve and plot the
express_precomputed("GBM")

# Retrieve only the data without plotting
data <- express_precomputed_tsne("GBM", just_return_data = TRUE)

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Title

Description

Title

Usage

express_sample_relatedness(
  data,
  method = "TSNE",
  gene_selector = "most_variable",
  sample_metadata = NULL,
  colour_by = NULL,
  perplexity = 30
)

Arguments

perplexity

if NULL, autocalculate

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