From 0935a7e307dc58eb1efaec4f37a349a7eb98abc5 Mon Sep 17 00:00:00 2001
From: Giulia Garcia <147185635+giuliaelgarcia@users.noreply.github.com>
Date: Tue, 16 Apr 2024 15:44:43 +0100
Subject: [PATCH] Update gene_list_format.md

---
 docs/usage/gene_list_format.md | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/docs/usage/gene_list_format.md b/docs/usage/gene_list_format.md
index e1df3016..790734bf 100644
--- a/docs/usage/gene_list_format.md
+++ b/docs/usage/gene_list_format.md
@@ -151,6 +151,33 @@ minimal:
 Generally in the visualization pipeline all gene groups in the input are plotted. In heatmaps and dotplots, one dotplot per group is plotted. For UMAPs, one plot per gene is
 plotted, and a new file is saved per group.
 
+
+## Plot Makers in the Visualization workflow 
+
+The custom maker csv file for full and minimal must contain three columns and follow the following structure: 
+  | mod  | feature  | group        |
+  |------|----------|--------------|
+  | prot | prot_CD8 | Tcellmarkers |
+  | rna  | CD8A     | Tcellmarkers |
+
+The full list will be plotted in dot plots and matrix plots, with one plot per group. 
+
+The shorter list will be plotted on umaps as well as other plot types, with one plot per group. 
+
+ | feature_1 | feature_2 | colour         |
+ |-----------|-----------|----------------|
+ | CD8A      | prot_CD8  |                |
+ | CD4       | CD8A      | doublet_scores |
+
+
+
+## Plot metadata variables 
+The scatter_features.csv file should have the following format:
+
+ | feature_1 | feature_2 | colour         |
+ |-----------|-----------|----------------|
+ |rna:total_counts | prot:total_counts  | doublet_scores
+
 ## Final notes
 
 Be deliberate and informative with the choice of group names for any gene set use, since the `.obs` column generated as output will be named based on the group of the gene list input file.