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Merged
tensulin merged 2 commits into from
Apr 1, 2026
Merged

nature styleguide requires reporting n's for all figures #19

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9bc4300
nature styleguide requires reporting n's for all figures
sjanssen2 Mar 31, 2026
967b098
ci: fix linting, config: remove old cluster fix
tensulin Apr 1, 2026
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17 changes: 16 additions & 1 deletion plotting/plot_include_orb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand All @@ -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,
Expand Down Expand Up @@ -1080,6 +1081,19 @@ 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,
Expand Down Expand Up @@ -1128,6 +1142,7 @@ def plot_block_correlation(
[0, 100, 200, 300, 400, 500, 1000, 2000, 3000],
labels=["0", "", "", "", "", "500", "1000", "2000", "3000"],
)

return fig


Expand Down
15 changes: 0 additions & 15 deletions test_nextflow.config
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Expand Up @@ -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
Expand Down
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