write_shiny_app: Create the ClustAssess ShinyApp

In Core-Bioinformatics/ClustAssess: Tools for Assessing Clustering

Create the ClustAssess ShinyApp

Description

Creates the ClustAssess ShinyApp based on the output of the automatic ClustAssess pipeline. In addition to that, the expression matrix and the metadata dataframe are provided as input to the ShinyApp.

Usage

write_shiny_app(
  object,
  metadata = NULL,
  assay_name = NULL,
  clustassess_object,
  project_folder,
  compression_level = 6,
  summary_function = stats::median,
  shiny_app_title = "",
  organism_enrichment = "hsapiens",
  height_ratio = 0.6,
  qualpalr_colorspace = "pretty"
)

## S3 method for class 'Seurat'
write_shiny_app(
  object,
  metadata = NULL,
  assay_name,
  clustassess_object,
  project_folder,
  compression_level = 6,
  summary_function = stats::median,
  shiny_app_title = "",
  organism_enrichment = "hsapiens",
  height_ratio = 0.6,
  qualpalr_colorspace = "pretty"
)

## Default S3 method:
write_shiny_app(
  object,
  metadata = NULL,
  assay_name = NULL,
  clustassess_object,
  project_folder,
  compression_level = 6,
  summary_function = stats::median,
  shiny_app_title = "",
  organism_enrichment = "hsapiens",
  height_ratio = 0.6,
  qualpalr_colorspace = "pretty"
)

Arguments

object	A Seurat object or an expression matrix
metadata	The metadata dataframe. This parameter will be ignored if the object is a Seurat object.
assay_name	The name of the assay to be used to extract the expression matrix from the Seurat object. This parameter will be ignored if the object is not a Seurat object.
clustassess_object	The output of the ClustAssess automatic pipeline
project_folder	The folder where the files will be written
compression_level	The compression level for the h5 files (See 'rhdf5::h5createFile“ for more details)
summary_function	The function used for summarizing the stability values; the default is median
shiny_app_title	The title of the shiny app
organism_enrichment	The organism used for the enrichment analysis; the default is hsapiens
height_ratio	The ratio of the height of the plot to the height of the browser; the default is 0.6
qualpalr_colorspace	The colorspace used for generating the colors; the default is pretty

Core-Bioinformatics/ClustAssess documentation built on Nov. 14, 2024, 6:33 p.m.