From 7ab200aacc24b53f0f10c32a2d5c77d01d2f4107 Mon Sep 17 00:00:00 2001 From: JeffreyMaurer Date: Thu, 10 Oct 2024 10:33:45 -0400 Subject: [PATCH] Added figure notes; nav orders multiplied by 10 for future insertion --- docs/Dry Lab SOPs/Basics.md | 2 +- docs/Dry Lab SOPs/Figures.md | 22 +++++++++++++++++++ docs/Dry Lab SOPs/Single-Cell_ATACseq.md | 2 +- docs/Dry Lab SOPs/Single-Cell_RNAseq.md | 2 +- docs/Dry Lab SOPs/Spatial_RNAseq.md | 2 +- docs/Intro to Computation/Bioinformatics.md | 2 +- .../ComputationResources.md | 2 +- docs/Intro to Computation/Programming.md | 2 +- docs/Intro to Computation/SourceControl.md | 2 +- docs/Onboarding/DryLabTraining.md | 2 +- docs/Onboarding/LabAccess.md | 2 +- docs/Onboarding/Prerequisites.md | 2 +- docs/Onboarding/WetLabTraining.md | 2 +- 13 files changed, 34 insertions(+), 12 deletions(-) create mode 100644 docs/Dry Lab SOPs/Figures.md diff --git a/docs/Dry Lab SOPs/Basics.md b/docs/Dry Lab SOPs/Basics.md index 4673fd3..7fd2090 100644 --- 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 new file mode 100644 index 0000000..9a585d4 --- /dev/null +++ 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. \ No newline at end of file diff --git a/docs/Dry Lab SOPs/Single-Cell_ATACseq.md b/docs/Dry Lab SOPs/Single-Cell_ATACseq.md index 2ce5f96..2fc5889 100644 --- 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 index d0d78b8..c23d087 100644 --- 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 index 67ef108..783b574 100644 --- 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 index 4a014d6..1525365 100644 --- 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 index 2117c6f..484c900 100644 --- 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 index 449c249..308822a 100644 --- 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 index 4e2704d..5f0e3d4 100644 --- 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 index 321f759..8b5b290 100644 --- 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 index e0cf3dc..d7c6524 100644 --- 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 index 9c08580..f7369df 100644 --- 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 index d19b4e4..c0b1741 100644 --- 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 ---