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Fix enrichment in compare plots and compare plot diffs #626

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Merged
kclem merged 1 commit into from
Mar 13, 2026
Merged

Fix enrichment in compare plots and compare plot diffs #626

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27 changes: 24 additions & 3 deletions .github/workflows/integration_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,9 @@ jobs:
pro: [false, true]
group:
- name: "Basic, Params, NHEJ"
filter: "basic or params or nhej_native_merge"
filter: "core"
- name: "Editors"
filter: "prime_editor or base_editor"
filter: "editor"
- name: "BAM"
filter: "bam"
- name: "Batch, Compare, Aggregate"
Expand Down Expand Up @@ -53,12 +53,33 @@ jobs:
path: .pixi
key: pixi-${{ runner.os }}-${{ runner.arch }}-test-${{ hashFiles('pixi.toml') }}

- name: Install MS core fonts
run: |
if [ -d ".pixi/msttcorefonts" ]; then
echo "Using cached fonts"
sudo mkdir -p /usr/share/fonts/truetype/msttcorefonts
sudo cp .pixi/msttcorefonts/* /usr/share/fonts/truetype/msttcorefonts/
else
echo "Installing fonts from scratch"
echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula select true" | sudo debconf-set-selections
sudo apt-get update
sudo apt-get install -y --no-install-recommends ttf-mscorefonts-installer
mkdir -p .pixi/msttcorefonts
cp /usr/share/fonts/truetype/msttcorefonts/*.ttf .pixi/msttcorefonts/
fi
sudo fc-cache -f

- name: Install environment
run: pixi install -e test

- name: Install CRISPResso
run: pixi run -e test install

- name: Rebuild pixi fontconfig cache and clear matplotlib font cache
run: |
pixi run -e test -- fc-cache -f
pixi run -e test -- python -c "import matplotlib; import shutil; shutil.rmtree(matplotlib.get_cachedir(), ignore_errors=True); print('Cleared', matplotlib.get_cachedir())"

- name: Checkout CRISPResso2_tests
uses: actions/checkout@v4
with:
Expand All @@ -80,4 +101,4 @@ jobs:
- name: Run Tests
run: |
pixi run -e test -- pytest CRISPResso2_tests/test_cli.py \
-k "${{ matrix.group.filter }}" -v ${{ matrix.pro && '--pro' || '' }} --test --print
-m "${{ matrix.group.filter }}" -v ${{ matrix.pro && '--pro' || '' }} ${{ !matrix.pro && '--diff-plots' || '' }} --test --print
36 changes: 23 additions & 13 deletions CRISPResso2/CRISPRessoCompareCORE.py
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Expand Up @@ -370,6 +370,8 @@ def get_plot_title_with_ref_name(plotTitle, refName):

# create merged heatmaps for each cut site
matching_allele_files = get_matching_allele_files(run_info_1, run_info_2)
# sort so regular allele files come before base edit files in the report
matching_allele_files.sort(key=lambda pair: 'base_edit' in pair[0])
for allele_file_1, allele_file_2 in matching_allele_files:
df1 = pd.read_csv(os.path.join(args.crispresso_output_folder_1, allele_file_1), sep="\t")
df2 = pd.read_csv(os.path.join(args.crispresso_output_folder_2, allele_file_2), sep="\t")
Expand All @@ -396,28 +398,36 @@ def get_plot_title_with_ref_name(plotTitle, refName):
merged[quant_cols] = merged[quant_cols].fillna(0)
lfc_error = 0.1
merged['each_LFC'] = np.log2(((merged['%Reads_' + sample_1_name] + lfc_error) / (merged['%Reads_' + sample_2_name] + lfc_error)).astype(float)).replace([np.inf, np.nan], 0)
merged = merged.sort_values(['%Reads_' + sample_1_name, 'Reference_Sequence', 'n_deleted', 'n_inserted', 'n_mutated'], ascending=False)
merged = merged.sort_values(['%Reads_' + sample_1_name, 'Aligned_Sequence', 'Reference_Sequence'], ascending=[False, True, True])
merged = merged.reset_index(drop=True).set_index('Aligned_Sequence')
args.crispresso_output_folder_root = os.path.split(allele_file_1)[1].replace(".txt", "")
allele_comparison_file = _jp(args.crispresso_output_folder_root + '.txt')
folder_root = os.path.split(allele_file_1)[1].replace(".txt", "")
allele_comparison_file = _jp(folder_root + '.txt')
merged.to_csv(allele_comparison_file, sep="\t", index=None)

plot_name = '3.' + args.crispresso_output_folder_root + '_top'
CRISPRessoPlot.plot_alleles_table_compare(ref_seq_around_cut, merged.sort_values(['each_LFC'], ascending=True), sample_1_name, sample_2_name, _jp(plot_name),
is_base_edit = 'base_edit' in allele_file_1
if is_base_edit:
title_prefix = 'Base edit comparison enriched in '
label_prefix = 'Base editing target nucleotide composition alleles.'
else:
title_prefix = 'Alleles enriched in '
label_prefix = 'Distribution comparison of alleles.'
label_suffix = ' Nucleotides are indicated by unique colors (A = green; C = red; G = yellow; T = purple). Substitutions are shown in bold font. Red rectangles highlight inserted sequences. Horizontal dashed lines indicate deleted sequences. The vertical dashed line indicates the predicted cleavage site. ' + \
'The proportion and number of reads is shown for each sample on the right, with the values for ' + sample_1_name + ' followed by the values for ' + sample_2_name + '.'

plot_name = '3.' + folder_root + '_top'
CRISPRessoPlot.plot_alleles_table_compare(ref_seq_around_cut, merged.sort_values(['each_LFC', 'Aligned_Sequence', 'Reference_Sequence'], ascending=[False, True, True]), sample_1_name, sample_2_name, _jp(plot_name),
MIN_FREQUENCY=args.min_frequency_alleles_around_cut_to_plot, MAX_N_ROWS=args.max_rows_alleles_around_cut_to_plot, SAVE_ALSO_PNG=save_png)
crispresso2_info['results']['general_plots']['summary_plot_names'].append(plot_name)
crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = 'Alleles enriched in ' + sample_1_name
crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = 'Distribution comparison of alleles. Nucleotides are indicated by unique colors (A = green; C = red; G = yellow; T = purple). Substitutions are shown in bold font. Red rectangles highlight inserted sequences. Horizontal dashed lines indicate deleted sequences. The vertical dashed line indicates the predicted cleavage site. ' + \
'The proportion and number of reads is shown for each sample on the right, with the values for ' + sample_1_name + ' followed by the values for ' + sample_2_name + '. Alleles are sorted for enrichment in ' + sample_1_name + '.'
crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = title_prefix + sample_1_name
crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = label_prefix + label_suffix + ' Alleles are sorted for enrichment in ' + sample_1_name + '.'
crispresso2_info['results']['general_plots']['summary_plot_datas'][plot_name] = [('Allele comparison table', os.path.basename(allele_comparison_file))]

plot_name = '3.' + args.crispresso_output_folder_root + '_bottom'
CRISPRessoPlot.plot_alleles_table_compare(ref_seq_around_cut, merged.sort_values(['each_LFC'], ascending=False), sample_1_name, sample_2_name, _jp(plot_name),
plot_name = '3.' + folder_root + '_bottom'
CRISPRessoPlot.plot_alleles_table_compare(ref_seq_around_cut, merged.sort_values(['each_LFC', 'Aligned_Sequence', 'Reference_Sequence'], ascending=[True, True, True]), sample_1_name, sample_2_name, _jp(plot_name),
MIN_FREQUENCY=args.min_frequency_alleles_around_cut_to_plot, MAX_N_ROWS=args.max_rows_alleles_around_cut_to_plot, SAVE_ALSO_PNG=save_png)
crispresso2_info['results']['general_plots']['summary_plot_names'].append(plot_name)
crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = 'Alleles enriched in ' + sample_2_name
crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = 'Distribution comparison of alleles. Nucleotides are indicated by unique colors (A = green; C = red; G = yellow; T = purple). Substitutions are shown in bold font. Red rectangles highlight inserted sequences. Horizontal dashed lines indicate deleted sequences. The vertical dashed line indicates the predicted cleavage site. ' + \
'The proportion and number of reads is shown for each sample on the right, with the values for ' + sample_1_name + ' followed by the values for ' + sample_2_name + '. Alleles are sorted for enrichment in ' + sample_2_name + '.'
crispresso2_info['results']['general_plots']['summary_plot_titles'][plot_name] = title_prefix + sample_2_name
crispresso2_info['results']['general_plots']['summary_plot_labels'][plot_name] = label_prefix + label_suffix + ' Alleles are sorted for enrichment in ' + sample_2_name + '.'
crispresso2_info['results']['general_plots']['summary_plot_datas'][plot_name] = [('Allele comparison table', os.path.basename(allele_comparison_file))]

debug('Calculating significant base counts...', {'percent_complete': 95})
Expand Down
1 change: 1 addition & 0 deletions pixi.toml
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Expand Up @@ -29,6 +29,7 @@ gxx_linux-64 = "*"
pytest = "*"
pytest-cov = "*"
pytest-check = "*"
pillow = "*"

[feature.test.pypi-dependencies]
ydiff = "*"
Expand Down
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