create_project: Create a configuration folder for a project

In tanaylab/MCView: A Shiny App for Metacell Analysis

Create a configuration folder for a project

Description

Create a project directory with the default configuration files and directory structure. If edit_config == TRUE, a text editor would be opened in order to edit the project config.yaml file.

Usage

create_project(
  project,
  title = "MCView",
  tabs = NULL,
  selected_gene1 = NULL,
  selected_gene2 = NULL,
  selected_mc1 = NULL,
  selected_mc2 = NULL,
  datasets = NULL,
  other_params = NULL,
  edit_config = TRUE,
  atlas = FALSE
)

Arguments

project	path of the project
title	The title of the app. This would be shown on the top left of the screen.
tabs	Controls which tabs to show in the left sidebar and their order. Options are: "QC", "Projection-QC", "Manifold", "Genes", "Query", "Atlas", "Markers", "Gene modules", "Projected-fold", "Diff. Expression", "Cell types", "Flow", "Annotate", "About". When NULL - default tabs would be set. For projects with atlas projections, please set atlas to TRUE.
selected_gene1, selected_gene2	The default genes that would be selected (in any screen with gene selection). If this parameter is missing, the 2 genes with highest max(expr)-min(expr) in the first dataset would be chosen.
selected_mc1, selected_mc2	The default metacells that would be selected in the Diff. Expression tab.
datasets	A named list with additional per-dataset parameters. Current parameters include default visualization properties of projection and scatter plots.
other_params	Named list of additional parameters such as projection_point_size, projection_point_stroke, scatters_point_size and scatters_stroke_size
edit_config	open file editor for config file editing
atlas	use default configuration for atlas projections (relevant only when tabs is NULL)

Examples

## Not run: 
dir.create("raw")
download.file(
    "http://www.wisdom.weizmann.ac.il/~atanay/metac_data/PBMC_processed.tar.gz",
    "raw/PBMC_processed.tar.gz"
)
untar("raw/PBMC_processed.tar.gz", exdir = "raw")
create_project("PBMC")

## End(Not run)

tanaylab/MCView documentation built on June 1, 2025, 8:08 p.m.