--- a
+++ b/settings.py
@@ -0,0 +1,179 @@
+import io
+import numpy as np
+import anndata as anndata
+import scipy as s
+import scanpy as sc
+import matplotlib.pyplot as plt
+import seaborn
+import pandas as pd
+import csv
+import os
+from dfply import *
+# from IPython.display import display
+from re import search
+from pathlib import Path
+import argparse
+
+#########
+## I/O ##
+#########
+
+io = {}
+
+host = os.uname()[1]
+if search("ricard", host):
+	io["basedir"] = "/Users/ricard/data/gastrulation_multiome_10x/test"
+	io["cellranger_output"] = "/Users/ricard/data/gastrulation_multiome_10x/original"
+	io["gene_metadata"] = "/Users/ricard/data/ensembl/mouse/v87/BioMart/all_genes/Mmusculus_genes_BioMart.87.txt"
+	io["gene_metadata_gtf"] = "/Users/ricard/data/ensembl/mouse/v98/GTF/Mus_musculus.GRCm38.98.gtf.gz"
+elif search("Workstation", host):
+    io["basedir"]="/home/lijingyu/gastrulation/data/gastrulation_multiome_10x"                   
+    io["gene_metadata"]='/home/lijingyu/gastrulation/data/ensembl/mouse/v87/BioMart/mRNA/Mmusculus_genes_BioMart.87.txt'
+elif search("BI2404M", host):
+	io["basedir"] = "/Users/argelagr/data/gastrulation_multiome_10x/test"
+	io["gene_metadata"] = "/Users/argelagr/data/ensembl/mouse/v87/BioMart/all_genes/Mmusculus_genes_BioMart.87.txt"
+elif search("pebble|headstone", host):
+	io["basedir"] = "/bi/group/reik/ricard/data/gastrulation_multiome_10x/test"
+	io["cellranger_output"] = "/bi/group/reik/ricard/data/gastrulation_multiome_10x/original"
+	io["gene_metadata"] = "/bi/group/reik/ricard/data/ensembl/mouse/v87/BioMart/all_genes/Mmusculus_genes_BioMart.87.txt"
+	io["gene_metadata_gtf"] = "/bi/group/reik/ricard/data/ensembl/mouse/v98/GTF/Mus_musculus.GRCm38.98.gtf.gz"
+	
+else:
+	print("Computer not recognised"); exit()
+
+io["metadata"] = io["basedir"] + "/sample_metadata.txt.gz"
+io["anndata"] = io["basedir"] + "/processed/rna/anndata.h5ad"
+io["anndata_scvelo"] = io["basedir"] + "/processed/rna/velocyto/anndata_scvelo.h5ad"
+
+#############
+## Options ##
+#############
+
+opts = {}
+
+opts["samples"] = [
+	"E7.5_rep1",
+	"E7.5_rep2",
+  	"E7.75_rep1",
+	"E8.0_rep1",
+	"E8.0_rep2",
+	"E8.5_rep1",
+	"E8.5_rep2",
+	"E8.75_rep1",
+	"E8.75_rep2",
+	"E8.5_CRISPR_T_KO",
+	"E8.5_CRISPR_T_WT"
+]
+
+
+opts["stages"] = [
+	"E7.5",
+	"E7.75",
+	"E8.0",
+	"E8.5",
+	"E8.75"
+]
+
+opts["celltypes"] = [
+	"Epiblast",
+	"Primitive_Streak",
+	"Caudal_epiblast",
+	"PGC",
+	"Anterior_Primitive_Streak",
+	"Notochord",
+	"Def._endoderm",
+	"Gut",
+	"Nascent_mesoderm",
+	"Mixed_mesoderm",
+	"Intermediate_mesoderm",
+	"Caudal_Mesoderm",
+	"Paraxial_mesoderm",
+	"Somitic_mesoderm",
+	"Pharyngeal_mesoderm",
+	"Cardiomyocytes",
+	"Allantois",
+	"ExE_mesoderm",
+	"Mesenchyme",
+	"Haematoendothelial_progenitors",
+	"Endothelium",
+	"Blood_progenitors_1",
+	"Blood_progenitors_2",
+	"Erythroid1",
+	"Erythroid2",
+	"Erythroid3",
+	"NMP",
+	"Rostral_neurectoderm",
+	"Caudal_neurectoderm",
+	"Neural_crest",
+	"Forebrain_Midbrain_Hindbrain",
+	"Spinal_cord",
+	"Surface_ectoderm",
+	"Visceral_endoderm",
+	"ExE_endoderm",
+	"ExE_ectoderm",
+	"Parietal_endoderm"
+]
+
+opts["celltype_colors"] = {
+	"Epiblast" : "#635547",
+	"Primitive_Streak" : "#DABE99",
+	"Caudal_epiblast" : "#9e6762",
+	"PGC" : "#FACB12",
+	"Anterior_Primitive_Streak" : "#c19f70",
+	"Notochord" : "#0F4A9C",
+	"Def._endoderm" : "#F397C0",
+	"Gut" : "#EF5A9D",
+	"Nascent_mesoderm" : "#C594BF",
+	"Mixed_mesoderm" : "#DFCDE4",
+	"Intermediate_mesoderm" : "#139992",
+	"Caudal_Mesoderm" : "#3F84AA",
+	"Paraxial_mesoderm" : "#8DB5CE",
+	"Somitic_mesoderm" : "#005579",
+	"Pharyngeal_mesoderm" : "#C9EBFB",
+	"Cardiomyocytes" : "#B51D8D",
+	"Allantois" : "#532C8A",
+	"ExE_mesoderm" : "#8870ad",
+	"Mesenchyme" : "#cc7818",
+	"Haematoendothelial_progenitors" : "#FBBE92",
+	"Endothelium" : "#ff891c",
+	"Blood_progenitors" : "#c9a997",
+	"Blood_progenitors_1" : "#f9decf",
+	"Blood_progenitors_2" : "#c9a997",
+	"Erythroid" : "#EF4E22",
+	"Erythroid1" : "#C72228",
+	"Erythroid2" : "#f79083",
+	"Erythroid3" : "#EF4E22",
+	"NMP" : "#8EC792",
+	"Neurectoderm" : "#65A83E",
+	"Rostral_neurectoderm" : "#65A83E",
+	"Caudal_neurectoderm" : "#354E23",
+	"Neural_crest" : "#C3C388",
+	"Forebrain_Midbrain_Hindbrain" : "#647a4f",
+	"Spinal_cord" : "#CDE088",
+	"Surface_ectoderm" : "#f7f79e",
+	"Visceral_endoderm" : "#F6BFCB",
+	"ExE_endoderm" : "#7F6874",
+	"ExE_ectoderm" : "#989898",
+	"Parietal_endoderm" : "#1A1A1A"
+}
+
+# opts["stages_colors"] = {
+# 	'E6.5':"#D53E4F",
+# 	'E6.75':"#F46D43",
+# 	'E7.0':"#FDAE61",
+# 	'E7.5':"#FFFFBF",
+# 	'E7.25':"#FEE08B",
+# 	'E7.75':"#E6F598",
+# 	'E8.0':"#ABDDA4",
+# 	'E8.5':"#3288BD",
+# 	'E8.25':"#66C2A5",
+# 	'mixed_gastrulation': "#A9A9A9"  
+# }
+
+opts["stage_colors"] = {
+	'E7.5':"#440154FF",
+	'E7.75':"#E6F598",
+	'E8.0':"#31688EFF",
+	'E8.5':"#35B779FF",
+	'E8.75':"#FDE725FF"
+}