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Create a configuration folder for a project

Source: R/project.R
create_project.Rd

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,
  help = FALSE,
  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.

help

Controls wether to start the app with a help modal (from introjs). Help messages can be edited in help.yaml file (see 'Architecture' vignette).

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

if (FALSE) {
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")
}