Added figure notes; nav orders multiplied by 10 for future insertion

yuyanchenglab · Oct 10, 2024 · 7ab200a · 7ab200a
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diff --git a/docs/Dry Lab SOPs/Basics.md b/docs/Dry Lab SOPs/Basics.md
@@ -3,7 +3,7 @@ layout: default
 title: Basics
 parent: Dry Lab SOPs
 has_children: false
-nav_order: 1
+nav_order: 10
 ---
 
 # {{page.title}}

diff --git a/docs/Dry Lab SOPs/Figures.md b/docs/Dry Lab SOPs/Figures.md
@@ -0,0 +1,22 @@
+---
+layout: default
+title: Figures
+parent: Dry Lab SOPs
+has_children: false
+nav_order: 20
+---
+
+# {{page.title}}
+
+## Principles for Figure Design
+
+We want our results to meet publishing guidelines, be presented their intended meaning clearly and be aesthetically pleasing. For that, there are a couple of things to keep in mind.
+
+* Figures are often no bigger than 3 x 3. Both R and python allow you to manually adjust the size of your figures overall and the size of the plotting panel within the image. Text is often kept below 10 pt font Arial.
+* Save as PDF. The PDF format allows manipulated without affecting the underlying data. Alterations such as rescaling and moving the legend are done in Illustrator by Yuyan. The PDF's from R are typically easier to adjust, so prefer plotting in R.
+* Done is better than perfect, and what is perfect to you will likely not match guidelines and require additional adjustment after consulting Yuyan.
+* When plotting retina cells, keep them in anatomical order: RGC, AC, HC, BC, MG, Cone, Rod, Endothelial, Astrocytes, Microglia
+
+## ChengLabThemes
+
+This is an R package installed locally on the HPC server and contains many helper functions for creating figures for the lab that match previous work.
diff --git a/docs/Dry Lab SOPs/Single-Cell_ATACseq.md b/docs/Dry Lab SOPs/Single-Cell_ATACseq.md
@@ -3,7 +3,7 @@ layout: default
 title: Single-Cell ATACseq
 parent: Dry Lab SOPs
 has_children: false
-nav_order: 2
+nav_order: 50
 ---
 
 # {{page.title}}

diff --git a/docs/Dry Lab SOPs/Single-Cell_RNAseq.md b/docs/Dry Lab SOPs/Single-Cell_RNAseq.md
@@ -3,7 +3,7 @@ layout: default
 title: Single-Cell RNAseq
 parent: Dry Lab SOPs
 has_children: false
-nav_order: 1
+nav_order: 30
 ---
 
 # {{page.title}}

diff --git a/docs/Dry Lab SOPs/Spatial_RNAseq.md b/docs/Dry Lab SOPs/Spatial_RNAseq.md
@@ -3,7 +3,7 @@ layout: default
 title: Spatial RNAseq
 parent: Dry Lab SOPs
 has_children: false
-nav_order: 3
+nav_order: 40
 ---
 
 # {{page.title}}

diff --git a/docs/Intro to Computation/Bioinformatics.md b/docs/Intro to Computation/Bioinformatics.md
@@ -1,7 +1,7 @@
 ---
 layout: default
 title: Intro to Bioinformatics
-nav_order: 4
+nav_order: 40
 parent: Intro to Computation
 has_children: false
 ---

diff --git a/docs/Intro to Computation/ComputationResources.md b/docs/Intro to Computation/ComputationResources.md
@@ -1,7 +1,7 @@
 ---
 layout: default
 title: Intro to Computational Resources
-nav_order: 1
+nav_order: 10
 parent: Intro to Computation
 has_children: false
 ---

diff --git a/docs/Intro to Computation/Programming.md b/docs/Intro to Computation/Programming.md
@@ -1,7 +1,7 @@
 ---
 layout: default
 title: Intro to Programming
-nav_order: 2
+nav_order: 20
 parent: Intro to Computation
 has_children: false
 ---

diff --git a/docs/Intro to Computation/SourceControl.md b/docs/Intro to Computation/SourceControl.md
@@ -1,7 +1,7 @@
 ---
 layout: default
 title: Source Control
-nav_order: 3
+nav_order: 30
 parent: Intro to Computation
 has_children: false
 ---

diff --git a/docs/Onboarding/DryLabTraining.md b/docs/Onboarding/DryLabTraining.md
@@ -1,7 +1,7 @@
 ---
 layout: default
 title: Dry Lab Training
-nav_order: 4
+nav_order: 40
 parent: Onboarding
 has_children: false
 ---

diff --git a/docs/Onboarding/LabAccess.md b/docs/Onboarding/LabAccess.md
@@ -1,7 +1,7 @@
 ---
 layout: default
 title: Lab Access
-nav_order: 2
+nav_order: 20
 parent: Onboarding
 has_children: false
 ---

diff --git a/docs/Onboarding/Prerequisites.md b/docs/Onboarding/Prerequisites.md
@@ -1,7 +1,7 @@
 ---
 layout: default
 title: Prerequisites
-nav_order: 1
+nav_order: 10
 parent: Onboarding
 has_children: false
 ---

diff --git a/docs/Onboarding/WetLabTraining.md b/docs/Onboarding/WetLabTraining.md
@@ -1,7 +1,7 @@
 ---
 layout: default
 title: Wet Lab Training
-nav_order: 3
+nav_order: 30
 parent: Onboarding
 has_children: false
 ---