From 0cafbbbb802ff31ecf9348678d3c3437a712b987 Mon Sep 17 00:00:00 2001
From: Alexis Simon <alexis.simon@normalesup.org>
Date: Thu, 7 Dec 2023 17:00:03 -0800
Subject: [PATCH] tweak cov/var inter rec plot

---
 workflow/Snakefile                              |  4 +++-
 workflow/scripts/plot_variable_intervals_rec.py | 11 +++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index fbe1322..cf8fd75 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -113,6 +113,7 @@ rule figure_intervals_rec_gss:
 		prefix = "results/simulations/sim_slim_sel_inter_2A_gradual_t140_s3.0",
 		rec = config['rec'],
 		intervals = config['intervals'],
+		model = "BGS",
 	conda:
 		"envs/popgensim.yaml"
 	script:
@@ -121,7 +122,7 @@ rule figure_intervals_rec_gss:
 rule figure_intervals_rec_bgs:
 	input:
 		expand(
-			'results/simulations/sim_msprime_inter_2A_r{rec}_i{inter}.pickle',
+			'results/simulations/sim_slim_bgs_scenario_2A_r{rec}_i{inter}.pickle',
 			rec=config['rec'],
 			inter=config['intervals'],
 		),
@@ -131,6 +132,7 @@ rule figure_intervals_rec_bgs:
 		prefix = "results/simulations/sim_slim_bgs_scenario_2A",
 		rec = config['rec'],
 		intervals = config['intervals'],
+		model = "BGS",
 	conda:
 		"envs/popgensim.yaml"
 	script:
diff --git a/workflow/scripts/plot_variable_intervals_rec.py b/workflow/scripts/plot_variable_intervals_rec.py
index de870de..2035bc3 100644
--- a/workflow/scripts/plot_variable_intervals_rec.py
+++ b/workflow/scripts/plot_variable_intervals_rec.py
@@ -2,6 +2,11 @@
 import numpy as np
 import matplotlib.pyplot as plt
 import pickle
+# sci notation formatter
+import matplotlib.ticker as tkr
+formatter = tkr.ScalarFormatter(useMathText=True)
+formatter.set_scientific(True)
+formatter.set_powerlimits((0, 0))
 
 colors_oi = [
     '#000000', # black
@@ -68,14 +73,20 @@
 axs[0].legend(ncols=3)
 axs[0].set_xlabel("sampling interval (gen)")
 axs[0].set_ylabel("Sum(Cov)")
+axs[0].set_title("A", loc='left', fontdict={'fontweight': 'bold'})
+axs[0].set_title(f"Covariances {snakemake.params['model']}")
 _ = axs[0].set_ylim(ylim)
 axs[1].set_xlabel("sampling interval (gen)")
 axs[1].set_ylabel("Sum(Var)")
+axs[1].set_title("B", loc='left', fontdict={'fontweight': 'bold'})
+axs[1].set_title(f"Variances {snakemake.params['model']}")
 _ = axs[1].set_ylim(ylim)
 
 _ = axs[0].set_xticks([int(x) + 0.5 for x in intervals])
 _ = axs[0].set_xticklabels(intervals)
 _ = axs[1].set_xticks([int(x) + 0.5 for x in intervals])
 _ = axs[1].set_xticklabels(intervals)
+axs[0].yaxis.set_major_formatter(formatter)
+axs[1].yaxis.set_major_formatter(formatter)
 
 fig.savefig(snakemake.output['fig'])
\ No newline at end of file