pipeline_flowchart.Rmd

---
output:
  pdf_document: default
  html_document: default
---
```{r, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(tidyverse)
library(ggflowchart)
library(igraph)
library(rlang)
```

# General Flowchart for Preprocessing Pipeline
```{r, fig.width=8, fig.height=10}
data <- tibble::tibble(from = c("Define Data Properties & Locations, 
                                Create Directories, Prepare Phenotype Data (Script 1)",
                                "Import Raw DNAm (Script 2)",
                                "Quality Control (Script 3)",
                                "Check Matching Epigenetic Sex (Script 4)",
                                "Samples Exclusion (Script 5)",
                                "Filtering CpGs (Script 6)",
                                "Normalization (Script 7)",
                                "Removal of Outliers & Detection of Batch Effects (Script 8)",
                                "Correction of Technical Batch Effects - Filtered Data (Script 9)"),
                       to = c("Import Raw DNAm (Script 2)",
                              "Quality Control (Script 3)",
                                "Check Matching Epigenetic Sex (Script 4)",
                                "Samples Exclusion (Script 5)",
                                "Filtering CpGs (Script 6)",
                                "Normalization (Script 7)",
                                "Removal of Outliers & Detection of Batch Effects (Script 8)",
                                "Correction of Technical Batch Effects - Filtered Data (Script 9)",
                                "Correction of Technical Batch Effects - Unfiltered Data (Script 10)"))

ggflowchart(data, fill = "lightblue", colour = "black", text_colour = "black", text_size = 5,
            y_nudge = 0.4, x_nudge = 0.2) +
  theme(plot.title = element_text(size = 20, hjust = 0.5, face = "bold"))
```