vignettes/articles/Misc_Functions.Rmd
Misc_Functions.RmdscCustomize has a number of other functions which users may find helpful or can adapt for their own uses.
# Load Packages
library(ggplot2)
library(dplyr)
library(magrittr)
library(patchwork)
library(Seurat)
library(scCustomize)In addition to aiding reproducibility through use of functions and reducing copy-paste errors scCustomize also contains function to aid in project setup which can be highly beneficial.
The function Setup_scRNAseq_Project() project serves as
example for how to setup reproducible project structure just using R
(although could be similarly achieved using shell script) but this way
makes it very easy to use with RStudio Projects workflow. For more
info on RStudio Project-oriented workflow see excellent overviews from
Jennifer
Bryan and Jim Hester’s: What They Forgot to Teach You About R and RStudio
Team
The function is very simple with just simple function call that requires no additional parameters:
This function will then create the following directory structure inside the working directory:
Working_Directory
├── 01_scripts
├── 02_raw_data
├── 03_meta_data
├── 04_data_objects
├── 05_plots
│ └── 01_QC_plots
│ └── 02_Round01_plots
│ └── 03_Round02_plots
├── 06_cluster_annotation
├── 07_csv_outputs
├── 08_final_plots_for_figurescustom_dir_file allows you to supply a delimited file
containing desired directory structure instead of default above.cluster_annotation_path and
cluster_annotation_file_name will create a cluster
annotation file using Create_Cluster_Annotation_File at
desired path.This function is the basic setup that I use for most projects but
everyone has their own style. Instead of requiring you to call
custom_dir_file every time I hope that this function might
serve as example that users can modify defaults and implement in their
own workflows. The function code is very simple to modify to any desired
structure.
NOTE: If you do modify for you our own please remember to attribute code to scCustomize package and cite appropriately.