diff --git a/Dockerfile b/Dockerfile index 73c158f..8275025 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,3 +21,5 @@ RUN pip install -U /tmp/scoary/scoary_2-$SCOARY_VERSION-py3-none-any.whl && \ ENV NUMBA_CACHE_DIR=/tmp/NUMBA_CACHE_DIR ENV CONFINT_DB=/tmp/CONFINT_DB ENV MPLCONFIGDIR=/tmp/MPLCONFIGDIR + +WORKDIR /data diff --git a/README.md b/README.md index 246154e..1ceef1e 100644 --- a/README.md +++ b/README.md @@ -17,19 +17,6 @@ association per trait. The results can be explored interactively with a simple, - [Understanding the p values](https://github.com/MrTomRod/scoary-2/wiki/Understanding-the-p-values) - [Usage as Python library](https://github.com/MrTomRod/scoary-2/wiki/Usage-as-Python-library) -# Todo: - -- [X] Binarize traits during multiprocessing -- [X] Idea: min_qval * min_empirical_p as new score -- [X] Improve messaging and logging -- [X] Remove multiple_testing_picking, more like Scoary 1 syntax? -- [X] Log runtime? -- [X] Refactoring -- [X] `overview.html`: go to function, popover always left -- [X] `overview.html` & `trait.html`: ~~set proper title~~, add logo/favicon -- [ ] `overview.html` & `trait.html`: link to `summary.tsv` / `coverage-matrix.tsv` / `result.tsv` download -- [X] Create wiki - [orthofinder]: https://github.com/davidemms/OrthoFinder/ [roary]: https://sanger-pathogens.github.io/Roary/ diff --git a/poetry.lock b/poetry.lock index a5ff677..65adc30 100644 --- a/poetry.lock +++ b/poetry.lock @@ -14,7 +14,7 @@ requests = ">=2.12" [[package]] name = "certifi" -version = "2022.9.24" +version = "2022.12.7" description = "Python package for providing Mozilla's CA Bundle." category = "dev" optional = false @@ -22,32 +22,29 @@ python-versions = ">=3.6" [[package]] name = "charset-normalizer" -version = "2.1.1" +version = "3.1.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "dev" optional = false -python-versions = ">=3.6.0" - -[package.extras] -unicode_backport = ["unicodedata2"] +python-versions = ">=3.7.0" [[package]] name = "contourpy" -version = "1.0.5" +version = "1.0.7" description = "Python library for calculating contours of 2D quadrilateral grids" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] numpy = ">=1.16" [package.extras] -test-no-codebase = ["pillow", "matplotlib", "pytest"] -test-minimal = ["pytest"] -test = ["isort", "flake8", "pillow", "matplotlib", "pytest"] -docs = ["sphinx-rtd-theme", "sphinx", "docutils (<0.18)"] -bokeh = ["selenium", "bokeh"] +bokeh = ["bokeh", "chromedriver", "selenium"] +docs = ["furo", "sphinx-copybutton"] +mypy = ["contourpy", "docutils-stubs", "mypy (==0.991)", "types-pillow"] +test = ["matplotlib", "pillow", "pytest"] +test-no-images = ["pytest"] [[package]] name = "cycler" @@ -87,14 +84,14 @@ termcolor = "*" [[package]] name = "fonttools" -version = "4.37.3" +version = "4.39.0" description = "Tools to manipulate font files" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] -all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=14.0.0)", "xattr"] +all = ["fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "zopfli (>=0.1.4)", "lz4 (>=1.7.4.2)", "matplotlib", "sympy", "skia-pathops (>=0.5.0)", "uharfbuzz (>=0.23.0)", "brotlicffi (>=0.8.0)", "scipy", "brotli (>=1.0.1)", "munkres", "unicodedata2 (>=15.0.0)", "xattr"] graphite = ["lz4 (>=1.7.4.2)"] interpolatable = ["scipy", "munkres"] lxml = ["lxml (>=4.0,<5)"] @@ -104,7 +101,7 @@ repacker = ["uharfbuzz (>=0.23.0)"] symfont = ["sympy"] type1 = ["xattr"] ufo = ["fs (>=2.2.0,<3)"] -unicode 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python-versions = ">=3.8" [package.extras] -default = ["numpy (>=1.19)", "scipy (>=1.8)", "matplotlib (>=3.4)", "pandas (>=1.3)"] -developer = ["pre-commit (>=2.20)", "mypy (>=0.961)"] -doc = ["sphinx (>=5)", "pydata-sphinx-theme (>=0.9)", "sphinx-gallery (>=0.10)", "numpydoc (>=1.4)", "pillow (>=9.1)", "nb2plots (>=0.6)", "texext (>=0.6.6)"] -extra = ["lxml (>=4.6)", "pygraphviz (>=1.9)", "pydot (>=1.4.2)", "sympy (>=1.10)"] -test = ["pytest (>=7.1)", "pytest-cov (>=3.0)", "codecov (>=2.1)"] +default = ["numpy (>=1.20)", "scipy (>=1.8)", "matplotlib (>=3.4)", "pandas (>=1.3)"] +developer = ["pre-commit (>=2.20)", "mypy (>=0.991)"] +doc = ["sphinx (==5.2.3)", "pydata-sphinx-theme (>=0.11)", "sphinx-gallery (>=0.11)", "numpydoc (>=1.5)", "pillow (>=9.2)", "nb2plots (>=0.6)", "texext (>=0.6.7)"] +extra = ["lxml (>=4.6)", "pygraphviz (>=1.10)", "pydot (>=1.4.2)", "sympy (>=1.10)"] +test = ["pytest (>=7.2)", "pytest-cov (>=4.0)", "codecov (>=2.1)"] [[package]] name = "numba" @@ -204,18 +201,15 @@ python-versions = ">=3.8" [[package]] name = "packaging" -version = "21.3" +version = "23.0" description = "Core utilities for Python packages" category = "main" optional = false -python-versions = ">=3.6" - -[package.dependencies] -pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" +python-versions = ">=3.7" [[package]] name = "pandas" -version = "1.5.0" +version = "1.5.3" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -227,11 +221,11 @@ python-dateutil = ">=2.8.1" pytz = ">=2020.1" [package.extras] -test = ["pytest-xdist (>=1.31)", "pytest (>=6.0)", "hypothesis (>=5.5.3)"] +test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"] [[package]] name = "patsy" -version = "0.5.2" +version = "0.5.3" description = "A Python package for describing statistical models and for building design matrices." category = "main" optional = false @@ -246,14 +240,14 @@ test = ["pytest", "pytest-cov", "scipy"] [[package]] name = "pillow" -version = "9.2.0" +version = "9.4.0" description = "Python Imaging Library (Fork)" category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] +docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] [[package]] @@ -280,7 +274,7 @@ six = ">=1.5" [[package]] name = "pytz" -version = "2022.2.1" +version = "2022.7.1" description = "World timezone definitions, modern and historical" category = "main" optional = false @@ -288,7 +282,7 @@ python-versions = "*" [[package]] name = "requests" -version = "2.28.1" +version = "2.28.2" description = "Python HTTP for Humans." 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certainty_cutoff: float): @@ -290,7 +290,7 @@ def worker( new_ns = grasp_namespace(BinarizeTraitNamespace, ns) del ns - kmeans = KMeans(n_clusters=2, random_state=new_ns.random_state) + kmeans = KMeans(n_init='auto', n_clusters=2, random_state=new_ns.random_state) gm = GaussianMixture(n_components=2, random_state=new_ns.random_state, covariance_type=new_ns.covariance_type) if new_ns.method == 'kmeans': diff --git a/scoary/scoary.py b/scoary/scoary.py index 91479f0..f60c4bd 100644 --- a/scoary/scoary.py +++ b/scoary/scoary.py @@ -38,10 +38,10 @@ def scoary( :param traits: Path to trait presence/absence table: columns=traits, rows=isolates :param outdir: Directory to place output files :param multiple_testing: "method:cutoff" for filtering genes after Fisher's test, where cutoff is a number that - specifies the FWER and method is one of [bonferroni, sidak, holm-sidak, holm, simes-hochberg, hommel, fdr_bh, - fdr_by, fdr_tsbh, fdr_tsbky]. Alternatively, the method can be 'native': then, the cutoff targets the uncorrected - pvalue from Fisher's test. - :param worst_cutoff: Drop traits if no gene with "worst" pvalue lower than threshold. Recommended if + specifies the FWER and method is one of [native, bonferroni, sidak, holm-sidak, holm, simes-hochberg, hommel, + fdr_bh, fdr_by, fdr_tsbh, fdr_tsbky]. Alternatively, the method can be 'native': then, the cutoff targets the + uncorrected p-value from Fisher's test. + :param worst_cutoff: Drop traits if no gene with "worst" p-value lower than threshold. Recommended if dataset contains multiple species :param max_genes: Keep only n highest-scoring genes in Fisher's test. Recommended if dataset is big and contains multiple species; avoids waisting computational resources on traits that simply correlate with phylogeny diff --git a/scoary/templates/overview.css b/scoary/templates/overview.css index 9ef7610..831be3f 100644 --- a/scoary/templates/overview.css +++ b/scoary/templates/overview.css @@ -1,36 +1,56 @@ -/*#popoverTable, th , td{*/ -/* width: 100%;*/ -/* border: 1px solid;*/ -/*}*/ +#grid { + display: grid; + width: 100%; + height: 100vh; + grid-template-columns: 4fr 5fr; +} .left { - /*float: left;*/ + height: 100vh; + min-width: 610px; + max-width: 770px; + overflow: scroll; } .right { - float: right + height: 100vh; + min-width: 400px; + display: flex; + flex-direction: column; + justify-content: space-between; + overflow-y: auto; } -.right-container { - position: fixed; - display: grid; - right: 0; - transform: translateY(-50%); - top: 50%; +.btn { + margin-top: 5px; +} + +#trait-select { + padding: 1rem; + margin-bottom: 1rem; } -.popover { - max-width: 550px; - max-height: 100%; - overflow: auto; +#trait-info { + margin-bottom: 1rem; + overflow-y: scroll; } -.popover-header a { - color: unset +#trait-info h2 a { + color: unset; + text-decoration: unset; + display: flex; + justify-content: space-between; + margin: 0; + padding: 0; } -#highlighter { - width: 12rem; +#trait-info h2 button { + margin: 0; +} + +#svg-container { + overflow-y: scroll; + overflow-x: hidden; } .placeholder { @@ -38,34 +58,34 @@ background-color: unset; } -/* imitate bootstrap container shrinking */ -@media (min-width: 576px) { - .right-container { - max-width: 540px; - } +#legend { + margin-bottom: 0.7rem; } -@media (min-width: 768px) { - .right-container { - max-width: 720px; - } +#legend td, #legend th { + text-align: center; + padding: 0 3px 0 3px; } -@media (min-width: 992px) { - .right-container { - max-width: 960px; - } +#legend th { + font-weight: bold; } +#legend-link { + color: unset; + text-decoration: unset; +} -@media (min-width: 1200px) { - .right-container { - max-width: 1140px; - } +#legend-link h3 { + text-align: center; } -@media (min-width: 1400px) { - .right-container { - max-width: 1320px; - } +.legend-title { + display: flex; } + +.legend-title .btn { + padding: 1px 8px 1px 8px; + margin-left: 5px; + margin-top: 2px; +} \ No newline at end of file diff --git a/scoary/templates/overview.html b/scoary/templates/overview.html index 3efd7cd..c706af2 100644 --- a/scoary/templates/overview.html +++ b/scoary/templates/overview.html @@ -8,16 +8,15 @@ - - + - @@ -27,21 +26,53 @@ -
- -

Traits dendrogram

- -
- - - - - -
- - -
- +
+
+
+

Traits dendrogram

+
+
+
+
+
+ +
+ + + +
+
+ +
+ +
+ +
+ +
+

Legend

+ + + +
+ +

The plot is log10-scaled.

+ + + + + + + + + + + + +
fe✱
Fisher's q-valueEmpirical p-valuefq*ep score
+ +
+
diff --git a/scoary/templates/overview.js b/scoary/templates/overview.js index 4e0f0bb..f7dcb2f 100644 --- a/scoary/templates/overview.js +++ b/scoary/templates/overview.js @@ -6,9 +6,8 @@ for (const attr of ['table', 'thead', 'tbody', 'tr', 'td', 'th']) { } const svgContainer = document.getElementById('svg-container') -let svgDocument -let overviewDf -let patches +const traitInfoDiv = document.getElementById('trait-info') +let svgDocument, overviewDf, patches /** @@ -56,11 +55,6 @@ const loadSvgPromise = fetch('overview_plot.svg', {method: 'GET', headers: {}}). console.warn(this, err) }) -function createTooltipTitle() { - const elementIndex = this.getAttribute('index') - const traitName = overviewDf['index'][elementIndex] - return `${traitName}` -} const isFloat = (n) => { n = parseFloat(n) @@ -68,11 +62,18 @@ const isFloat = (n) => { return Number(n) === n && n % 1 !== 0 } -function createTooltipContent() { - const elementIndex = this.getAttribute('index') +function createTooltipContent(elementIndex) { const traitData = overviewDf.data[elementIndex] + const traitName = overviewDf['index'][elementIndex] - let html = '' + let html = `

${traitName} + +

` + + html += '
' overviewDf.meta.fields.forEach((key, i) => { if (key === 'Trait') return @@ -95,38 +96,12 @@ function createTooltipContent() { } Promise.all([loadSvgPromise, overviewPromise]).then(() => { - const openPopovers = [] const patchesElement = document.getElementById('clickable-patches') - const hideAllPopovers = () => { - while (openPopovers.length) { - const target = openPopovers.pop() - bootstrap.Popover.getInstance(target).hide() - } - } patchesElement.addEventListener('mouseover', function (event) { - let instance = bootstrap.Popover.getInstance(event.target) - if (instance === null) { - instance = new bootstrap.Popover(event.target, { - container: 'body', - trigger: 'manual', - placement: 'right', - html: true, - title: createTooltipTitle, - content: createTooltipContent, - }) - } - - instance.show() - hideAllPopovers() - openPopovers.push(event.target) + traitInfoDiv.innerHTML = createTooltipContent(event.target.getAttribute('index')) }) patchesElement.addEventListener('auxclick', openTraitsTab) - document.addEventListener('click', function (event) { - const isPopoverOrSvg = event.target.closest('.popover, svg') !== null - if (isPopoverOrSvg) return - hideAllPopovers() - }) Array.from(patchesElement.children).forEach((patch, index) => { patch.setAttribute('index', index) }) @@ -144,9 +119,10 @@ function openTraitsTab(event) { window.open(url, '_blank').focus() } -let ax4 +let ax4, slimSelect const selected = [] +// toggle trait yellow const toggleTrait = (eventOrId) => { let target, index if (Number.isInteger(eventOrId)) { @@ -205,6 +181,12 @@ const deselectAll = () => { } } +const goToTrait = () => { + const selectId = parseInt(slimSelect.selected()) + const target = ax4.children[selectId] + target.scrollIntoView() +} + // // activate clickable boxes Promise.all([loadSvgPromise, overviewPromise] ).then(([result, __]) => { @@ -217,7 +199,7 @@ Promise.all([loadSvgPromise, overviewPromise] ax4 = document.getElementById('clickable-patches') - const slimSelect = new SlimSelect({ + slimSelect = new SlimSelect({ select: '#slim-select', placeholder: 'Click here to select traits', data: overviewDf.index.map((trait, index) => { @@ -226,6 +208,11 @@ Promise.all([loadSvgPromise, overviewPromise] onChange: function () { const selectId = parseInt(slimSelect.selected()) toggleTrait(selectId) + console.log(selectId) + traitInfoDiv.innerHTML = createTooltipContent(selectId) }, }) + + const goToButton = document.getElementById('goto-button') + goToButton.addEventListener('click', goToTrait) }) diff --git a/scoary/templates/trait.css b/scoary/templates/trait.css index 6187c93..da8e7f0 100644 --- a/scoary/templates/trait.css +++ b/scoary/templates/trait.css @@ -105,3 +105,9 @@ code { .main-svg { background: unset !important; } + +.title-with-link { + display: flex; + justify-content: space-between; +} + diff --git a/scoary/templates/trait.html b/scoary/templates/trait.html index 0e499d5..792d80f 100644 --- a/scoary/templates/trait.html +++ b/scoary/templates/trait.html @@ -74,13 +74,30 @@

-

Genes

+
+

Genes

+ + + +
+
Toggle column:
-

Coverage matrix

+
+

Coverage matrix

+
+ + + + + + +
+
+
diff --git a/scoary/templates/trait.js b/scoary/templates/trait.js index 70d0b8c..dc35dcf 100644 --- a/scoary/templates/trait.js +++ b/scoary/templates/trait.js @@ -95,7 +95,13 @@ const documentReadyPromise = new Promise(function (resolve) { _domResolve = resolve }) document.addEventListener('DOMContentLoaded', _domResolve) -documentReadyPromise.then(() => document.querySelector('#trait-name').textContent = trait) +documentReadyPromise.then(() => { + document.querySelector('#trait-name').textContent = trait + // set the download links + document.getElementById('download-genes').href = `traits/${trait}/result.tsv` + document.getElementById('download-coverage-matrix').href = `traits/${trait}/coverage-matrix.tsv` + document.getElementById('download-values').href = `traits/${trait}/values.tsv` +}) /** @@ -178,7 +184,10 @@ const valuesPromise = configPromise.then(config => { header: true, download: true, skipEmptyLines: true, delimiter: '\t', newline: '\n', }).then((valuesData) => { valuesData.isNumeric = valuesData.meta.fields.includes('value') - if (!valuesData.isNumeric) document.getElementById('histogram-container').remove() + if (!valuesData.isNumeric) { + document.getElementById('histogram-container').remove() + document.getElementById('download-values').style.display = 'none' + } valuesData.isolateToTrait = Object.fromEntries(valuesData.data.map(x => [x['isolate'], x['class'].toLowerCase()])) if (valuesData.isNumeric) { valuesData.isolateToValue = Object.fromEntries(valuesData.data.map(x => [x['isolate'], x['value']])) diff --git a/tests/test_final_overview.py b/tests/test_final_overview.py index e30f018..e6a04b3 100644 --- a/tests/test_final_overview.py +++ b/tests/test_final_overview.py @@ -5,6 +5,22 @@ from scoary.load_traits import load_binary from scoary.utils import pd, AnalyzeTraitNamespace +REPLACE_COPIES_WITH_SYMLINKS = True + + +def replace_copies_with_symlinks(): + def repl(fn, relpath='../..', subdir='app'): + src = f'{relpath}/scoary/templates/{fn}' + target = f'../TEST_OUTPUT/{subdir}/{fn}' + if os.path.isfile(target): + os.remove(target) + os.symlink(src=src, dst=target) + + for file in ['trait.html', 'overview.html']: + repl(file, relpath='..', subdir='') + for file in ['config.json', 'favicon.svg', 'overview.css', 'overview.js', 'trait.css', 'trait.js']: + repl(file) + class Test(TestCase): def setUp(self) -> None: @@ -19,6 +35,8 @@ def setUp(self) -> None: os.makedirs(f'{self.temp_dir}/{dir_}', exist_ok=True) def tearDown(self) -> None: + if REPLACE_COPIES_WITH_SYMLINKS: + replace_copies_with_symlinks() print(f'Open file://{self.temp_dir} to see the result!') print(f'To clean up, run "rm -r {self.temp_dir}"') @@ -128,3 +146,8 @@ def x(a): print(d) x(a) + + +class ReplaceCopiesWithSymlinks(TestCase): + def test_replace_copies_with_symlinks(self): + replace_copies_with_symlinks()