From 9bc43002a7c53f6ee7197262b24608edae6ea17d Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 31 Mar 2026 18:00:08 +0200 Subject: [PATCH 1/2] nature styleguide requires reporting n's for all figures --- plotting/plot_include_orb.py | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/plotting/plot_include_orb.py b/plotting/plot_include_orb.py index 213c9d2..fcad2c8 100644 --- a/plotting/plot_include_orb.py +++ b/plotting/plot_include_orb.py @@ -1034,6 +1034,7 @@ def plot_block_correlation( assemblers = settings["labels"]["assemblers"] # 'Mann-Whitney', 't-test_ind', 'Wilcoxon' + block_colors = {"recovered": "lightgreen", "missed": "#dddddd"} for i, environment in tqdm(enumerate(environments), disable=not verbose, desc=f"Drawing panels for {field} plot"): ax = axes[i] plotdata = data_block_recovery[environment] @@ -1050,7 +1051,7 @@ def plot_block_correlation( x=field, hue="category", ax=ax, - palette={"recovered": "lightgreen", "missed": "#dddddd"}, + palette=block_colors, showfliers=False, hue_order=hue_order, order=ordered_assembler, @@ -1080,6 +1081,21 @@ def plot_block_correlation( fontweight="bold", ) + ns = plotdata.groupby(["assembler", "category"]).size() + ax_ns = ax.twinx() + ax_ns.set_ylim(ax.get_ylim()) + ns_labels = [] + ns_colors = [] + for ass_label in ordered_assembler: + for cat in hue_order: + ns_labels.append(f"n={ns.loc[ass_label, cat]:,}") + ns_colors.append({'lightgreen': 'darkgreen', '#dddddd': 'darkgray'}.get(block_colors[cat])) + ax_ns.set_yticks([x + offset for x in ax.get_yticks() for offset in [-0.2, 0.2]], + labels=ns_labels, + fontsize=8) + for color, label in zip(ns_colors, ax_ns.get_yticklabels()): + label.set_color(color) + if test is not None: annotator = Annotator( ax, @@ -1128,6 +1144,7 @@ def plot_block_correlation( [0, 100, 200, 300, 400, 500, 1000, 2000, 3000], labels=["0", "", "", "", "", "500", "1000", "2000", "3000"], ) + return fig From 967b098a83c477c230157cb2c7d2a4bb0321b558 Mon Sep 17 00:00:00 2001 From: Timo Wentong Lin Date: Wed, 1 Apr 2026 11:39:25 +0200 Subject: [PATCH 2/2] ci: fix linting, config: remove old cluster fix --- plotting/plot_include_orb.py | 6 ++---- test_nextflow.config | 15 --------------- 2 files changed, 2 insertions(+), 19 deletions(-) diff --git a/plotting/plot_include_orb.py b/plotting/plot_include_orb.py index fcad2c8..b0423e6 100644 --- a/plotting/plot_include_orb.py +++ b/plotting/plot_include_orb.py @@ -1089,10 +1089,8 @@ def plot_block_correlation( for ass_label in ordered_assembler: for cat in hue_order: ns_labels.append(f"n={ns.loc[ass_label, cat]:,}") - ns_colors.append({'lightgreen': 'darkgreen', '#dddddd': 'darkgray'}.get(block_colors[cat])) - ax_ns.set_yticks([x + offset for x in ax.get_yticks() for offset in [-0.2, 0.2]], - labels=ns_labels, - fontsize=8) + ns_colors.append({"lightgreen": "darkgreen", "#dddddd": "darkgray"}.get(block_colors[cat])) + ax_ns.set_yticks([x + offset for x in ax.get_yticks() for offset in [-0.2, 0.2]], labels=ns_labels, fontsize=8) for color, label in zip(ns_colors, ax_ns.get_yticklabels()): label.set_color(color) diff --git a/test_nextflow.config b/test_nextflow.config index fdc53e0..8583cbd 100644 --- a/test_nextflow.config +++ b/test_nextflow.config @@ -15,26 +15,11 @@ process { clusterOptions = '' // --exclude=rs700-bcf-5.intra //rs700-bcf-1.intra,rs700-bcf-4.intra beforeScript = """ - var=/var/scratch/\$USER/process_tmp_\$(date +%s%N)\$RANDOM - echo $USER >> log.txt - echo \$var > podman_dir.txt - mkdir -p \$var/podman - #podman system reset -f - #podman system migrate - export XDG_RUNTIME_DIR=\$var/podman - export TMPDIR=\$var export http_proxy=http://192.168.10.1:3128 export https_proxy=http://192.168.10.1:3128 export ftp_proxy=http://192.168.10.1:3128 """ - afterScript = """ - var=\$(cat podman_dir.txt) - echo \$var - rm -rf \$var - """ - - withName: SALMON_QUANT { memory = '32G' cpus = 32