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Create the ClustAssess ShinyApp

Source: R/generics.R, R/shiny-app.R
write_shiny_app.Rd

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. If the clustassess object is not provided, the function will create the light version of the ClustAssess ShinyApp, that will not contain the assessment results. For this case, the metadata parameter should contain two aditional columns named 'UMAP_1" and 'UMAP_2' that will correspond to the 2D embedding of the cells.

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",
  prompt_feature_choice = TRUE
)

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

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

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. If the ClustAssess object is not provided (NULL), the function will create the light version of the ShinyApp, that will not contain the assessment results.

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

prompt_feature_choice

Should the user be prompted to choose if he wants to continue with the selection of features even if it is lower than median sequence depth; the default is TRUE