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.
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 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"
)
# S3 method for default
write_shiny_app(
object,
metadata,
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"
)A Seurat object or an expression matrix
The metadata dataframe. This parameter will be ignored if the object is a Seurat object.
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.
The output of the ClustAssess automatic pipeline
The folder where the files will be written
The compression level for the h5 files (See `rhdf5::h5createFile`` for more details)
The function used for summarizing the stability values; the default is median
The title of the shiny app
The organism used for the enrichment analysis; the default is hsapiens
The ratio of the height of the plot to the height of the browser; the default is 0.6
The colorspace used for generating the colors; the default is pretty