Flowchart for selection of RPs

flowchart

Charleen D. Adams1 and Bernardo Lemos1,2

1Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
2Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA

Contents

# install.packages("DiagrammeR")
library(DiagrammeR)
library(DiagrammeRsvg)
library(magrittr)
library(rsvg)

0.1 Flowchart for selection of RP eQTLs

grViz(diagram = "digraph flowchart {
      # define node aesthetics
      node [fontname = Arial, shape = oval, color = Lavender, style = filled, fixedsize = false, width = 10, height= 3.5, fontsize = 30]        
      tab1 [label = '@@1']
      tab2 [label = '@@2']
      tab3 [label = '@@3']
      tab4 [label = '@@4']
      tab5 [label = '@@5']

      # set up node layout
      tab1 -> tab2;
      tab2 -> tab3;
      tab3 -> tab4;
      tab3 -> tab5
      }

      [1]: 'n=\\nRPs with eQTLs in exposure\\n--eQTLs not LD-clumped--\\n(eQTL P<0.05)'
      [2]: 'n=\\nRPs with eQTLs in exposure\\n--eQTLs not LD-clumped--\\n(eQTL P<5x10-06)'    
      [3]: 'n=\\nRPs with eQTLs in exposure & outcome\\n--eQTLs not LD-clumped--\\n(eQTL P<5x10-06)\\nFor:\\nWald ratios'     
      [4]: 'n=\\nRPs with eQTLs in exposure & outcome\\n--eQTLs LD-clumped per RP--\\n(eQTL P<5x10-06)\\nFor:\\nindividual-RP meta-analyses'
      [5]: 'n=\\nRPs  with eQTLs in exposure & outcome\\n--eQTLs LD-clumped across RPs--\\n (eQTL P<5x10-06)\\nFor:\\ncollective-RP meta-analyses'
      ")

#ggsave(filename = "/n/home04/cdadams/Aim2/flowchart/flowchart.png", dpi=300)

0.2 Skyblue option (not using)

# I don't like the skyblue and white font.

grViz(diagram = "digraph flowchart {
      # define node aesthetics
      node [fontname = Arial, shape = oval, color = DeepSkyBlue, style = filled, fontcolor = White, fixedsize = false, width = 10, height= 3.5, fontsize = 30]        
      tab1 [label = '@@1']
      tab2 [label = '@@2']
      tab3 [label = '@@3']
      tab4 [label = '@@4']
      tab5 [label = '@@5']

      # set up node layout
      tab1 -> tab2;
      tab2 -> tab3;
      tab3 -> tab4;
      tab3 -> tab5
      }

      [1]: 'n=\\nRPs with eQTLs in exposure\\n--eQTLs not LD-clumped--\\n(eQTL P<0.05)'
      [2]: 'n=\\nRPs  with eQTLs in exposure\\n--eQTLs not LD-clumped--\\n(eQTL P<5x10-06)'    
      [3]: 'n=\\nRPs  with eQTLs in exposure & outcome\\n--eQTLs not LD-clumped--\\n(eQTL P<5x10-06)\\nFor:\\nWald ratios'     
      [4]: 'n=\\nRPs with eQTLs in exposure & outcome\\n--eQTLs LD-clumped per RP--\\n(eQTL P<5x10-06)\\nFor:\\nindividual-RP meta-analyses'
      [5]: 'n=\\nRPs  with eQTLs in exposure & outcome\\n--eQTLs LD-clumped across RPs--\\n (eQTL P<5x10-06)\\nFor:\\ncollective-RP meta-analyses'
      ")

0.3 Bash

mkdir /n/home04/cdadams/Aim2/flowchart
cd /n/home04/cdadams/Aim2/flowchart

echo "## Flowchart for selecting RPs

### Rpubs: https://rpubs.com/Charleen_D_Adams/758188" 

<p align="center">
<img src="https://github.com/LabLemos/journalclub/blob/main/April192021/rif.jpeg" width="700" height="500">
</p>

>> README.md

# Helpful commands
#rm -rf .git
#rm README.md 

git add flowchart.Rmd
git commit -m "flowchart for RP selection"
git branch -M main
git push --all

git add flowchart.png
git commit -m "flowchart for RP selection: had to be saved as an html and screenshot"
git branch -M main
git push --all

git add README.md
git commit -m "README.md"
git branch -M main
git push --all