make_cellbrowser: Cell browser wrapper Builds cell browser with better defaults
In rnabioco/scbp: Boilerplate functions for single cell rna-seq analysis

make_cellbrowser

R Documentation

Cell browser wrapper Builds cell browser with better defaults

Description

Cell browser wrapper Builds cell browser with better defaults

Usage

make_cellbrowser(
  so,
  column_list = NULL,
  primary_color_palette = discrete_palette_default,
  secondary_color_palette = palette_OkabeIto,
  secondary_cols = NULL,
  outdir = "cellbrowser",
  project = "seurat",
  marker_file = NULL,
  ident = "clusters",
  embeddings = names(so@reductions),
  color_skip = NULL,
  skip_expr_matrix = FALSE,
  skip_markers = FALSE,
  overwrite_cb_config = TRUE,
  annotate_markers = TRUE,
  default_assay = "RNA",
  assays = NULL,
  cellbrowser_dir = "/miniconda3/bin/",
  description = NULL,
  config = NULL,
  summary_html_format = "**{title}**  \n{description}"
)

Arguments

`so`	seurat object
`column_list`	named vector of columns to keep in browser. Names will be displayed in the browser.
`primary_color_palette`	palette for catagorical variables
`secondary_color_palette`	secondary palette for catagorical variables
`secondary_cols`	columns to color by secondary_color_palette
`outdir`	output directory for cellbrowser
`project`	project string
`marker_file`	seurat marker file path
`ident`	default variable for labeling
`embeddings`	embeddings to show in browser
`color_skip`	no idea
`skip_expr_matrix`	dont overwrite expression matrix
`skip_markers`	dont overwrite markers
`overwrite_cb_config`	overwritec cellbrowser.conf file
`annotate_markers`	annotate markers using cellbrowser functionality
`default_assay`	assay to export (RNA)
`assays`	character vector of additional assay expression matrices to export. If supplied then the data matrix with be concatenated via rowbinding to the default assay matrix. If a named character vector is supplied the name will be prefixed to the rows (i.e features).
`cellbrowser_dir`	directory where cellbrowser binary lives
`description`	named list dataset descriptions. Will be written to desc.conf file. Title will default to the project title. See UCSC cellbrowser documentation for allowable entries.
`config`	named list with custom entries to add to cellbrowser.conf file. e.g. (config = list(priority = 1, radius = 5, alpha = 0.3)). See UCSC cellbrowser documentation for allowable entries.
`summary_html_format`	markdown formatted glue expression for formatting title and description into summary.html file