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