From ce528fe6f9c29fa2f5aeec865aa374a746d4f891 Mon Sep 17 00:00:00 2001 From: ahernank Date: Thu, 4 Jan 2024 15:39:51 +0000 Subject: [PATCH] include study IDs on 3.0 --- docs/ag3/ag3.0.ipynb | 801 +++++++++++++++++++++++++++++++------------ 1 file changed, 588 insertions(+), 213 deletions(-) diff --git a/docs/ag3/ag3.0.ipynb b/docs/ag3/ag3.0.ipynb index d588184..643651d 100644 --- a/docs/ag3/ag3.0.ipynb +++ b/docs/ag3/ag3.0.ipynb @@ -122,7 +122,298 @@ "remove-input" ] }, - "outputs": [], + "outputs": [ + { + "data": { + "application/javascript": [ + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " const force = true;\n", + "\n", + " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", + " root._bokeh_onload_callbacks = [];\n", + " root._bokeh_is_loading = undefined;\n", + " }\n", + "\n", + "const JS_MIME_TYPE = 'application/javascript';\n", + " const HTML_MIME_TYPE = 'text/html';\n", + " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", + " const CLASS_NAME = 'output_bokeh rendered_html';\n", + "\n", + " /**\n", + " * Render data to the DOM node\n", + " */\n", + " function render(props, node) {\n", + " const script = document.createElement(\"script\");\n", + " node.appendChild(script);\n", + " }\n", + "\n", + " /**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + " function handleClearOutput(event, handle) {\n", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\n", + " const cell = handle.cell;\n", + "\n", + " const id = cell.output_area._bokeh_element_id;\n", + " const server_id = cell.output_area._bokeh_server_id;\n", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(id)\n", + " }\n", + "\n", + " if (server_id !== undefined) {\n", + " // Clean up Bokeh references\n", + " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", + " cell.notebook.kernel.execute(cmd_clean, {\n", + " iopub: {\n", + " output: function(msg) {\n", + " const id = msg.content.text.trim()\n", + " drop(id)\n", + " }\n", + " }\n", + " });\n", + " // Destroy server and session\n", + " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", + " cell.notebook.kernel.execute(cmd_destroy);\n", + " }\n", + " }\n", + "\n", + " /**\n", + " * Handle when a new output is added\n", + " */\n", + " function handleAddOutput(event, handle) {\n", + " const output_area = handle.output_area;\n", + " const output = handle.output;\n", + "\n", + " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", + " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", + " return\n", + " }\n", + "\n", + " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + "\n", + " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", + " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", + " // store reference to embed id on output_area\n", + " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " }\n", + " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " const bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " const script_attrs = bk_div.children[0].attributes;\n", + " for (let i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + " }\n", + "\n", + " function register_renderer(events, OutputArea) {\n", + "\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " const toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[toinsert.length - 1]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " /* Handle when an output is cleared or removed */\n", + " events.on('clear_output.CodeCell', handleClearOutput);\n", + " events.on('delete.Cell', handleClearOutput);\n", + "\n", + " /* Handle when a new output is added */\n", + " events.on('output_added.OutputArea', handleAddOutput);\n", + "\n", + " /**\n", + " * Register the mime type and append_mime function with output_area\n", + " */\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " /* Is output safe? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded() {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " el.textContent = \"BokehJS is loading...\";\n", + " }\n", + " if (root.Bokeh !== undefined) {\n", + " if (el != null) {\n", + " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(display_loaded, 100)\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.3.0.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded() {\n const el = document.getElementById(null);\n if (el != null) {\n el.textContent = \"BokehJS is loading...\";\n }\n if (root.Bokeh !== undefined) {\n if (el != null) {\n el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(display_loaded, 100)\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.3.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.3.0.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "import malariagen_data\n", "ag3 = malariagen_data.Ag3()" @@ -282,7 +573,7 @@ " \n", " \n", " AG1000G-X\n", - " 297\n", + " 669\n", " \n", " \n", "\n", @@ -318,7 +609,7 @@ "AG1000G-MZ 74\n", "AG1000G-TZ 300\n", "AG1000G-UG 290\n", - "AG1000G-X 297" + "AG1000G-X 669" ] }, "execution_count": 3, @@ -346,7 +637,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "metadata": { "colab": { "base_uri": "https://localhost:8080/", @@ -381,6 +672,7 @@ " \n", " \n", " \n", + " \n", " taxon\n", " arabiensis\n", " coluzzii\n", @@ -388,10 +680,10 @@ " gcx1\n", " gcx2\n", " gcx3\n", - " intermediate_arabiensis_gambiae\n", - " intermediate_gambiae_coluzzii\n", + " unassigned\n", " \n", " \n", + " study_id\n", " sample_set\n", " country\n", " year\n", @@ -402,12 +694,12 @@ " \n", " \n", " \n", - " \n", " \n", " \n", " \n", " \n", " AG1000G-AO\n", + " AG1000G-AO\n", " Angola\n", " 2009\n", " 0\n", @@ -417,20 +709,19 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-BF-1\n", " AG1000G-BF-A\n", " Burkina Faso\n", " 2012\n", " 0\n", " 82\n", - " 98\n", + " 99\n", " 0\n", " 0\n", " 0\n", " 0\n", - " 1\n", " \n", " \n", " AG1000G-BF-B\n", @@ -443,9 +734,9 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-BF-2\n", " AG1000G-BF-C\n", " Burkina Faso\n", " 2004\n", @@ -456,10 +747,10 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " AG1000G-CD\n", + " AG1000G-CD\n", " Democratic Republic of the Congo\n", " 2015\n", " 0\n", @@ -469,10 +760,10 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " AG1000G-CF\n", + " AG1000G-CF\n", " Central African Republic\n", " 1993\n", " 0\n", @@ -482,7 +773,6 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " 1994\n", @@ -493,10 +783,10 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " AG1000G-CI\n", + " AG1000G-CI\n", " Cote d'Ivoire\n", " 2012\n", " 0\n", @@ -506,9 +796,9 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-CM-1\n", " AG1000G-CM-A\n", " Cameroon\n", " 2009\n", @@ -519,9 +809,9 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-CM-2\n", " AG1000G-CM-B\n", " Cameroon\n", " 2005\n", @@ -532,9 +822,9 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-CM-3\n", " AG1000G-CM-C\n", " Cameroon\n", " 2013\n", @@ -545,10 +835,10 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " AG1000G-FR\n", + " AG1000G-FR\n", " Mayotte\n", " 2011\n", " 0\n", @@ -558,9 +848,9 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-GA-1\n", " AG1000G-GA-A\n", " Gabon\n", " 2000\n", @@ -571,10 +861,10 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " AG1000G-GH\n", + " AG1000G-GH\n", " Ghana\n", " 2012\n", " 0\n", @@ -584,9 +874,9 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-GM-1\n", " AG1000G-GM-A\n", " Gambia, The\n", " 2011\n", @@ -597,22 +887,22 @@ " 6\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-GM-2\n", " AG1000G-GM-B\n", " Gambia, The\n", - " 2012\n", + " 2006\n", " 0\n", - " 2\n", " 0\n", - " 9\n", - " 20\n", " 0\n", + " 9\n", + " 22\n", " 0\n", " 0\n", " \n", " \n", + " AG1000G-GM-3\n", " AG1000G-GM-C\n", " Gambia, The\n", " 2012\n", @@ -623,20 +913,19 @@ " 172\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-GN-ML\n", " AG1000G-GN-A\n", " Guinea\n", " 2012\n", " 0\n", - " 3\n", - " 40\n", + " 4\n", + " 41\n", + " 0\n", " 0\n", - " 1\n", " 0\n", " 0\n", - " 1\n", " \n", " \n", " AG1000G-GN-B\n", @@ -644,27 +933,26 @@ " 2012\n", " 0\n", " 7\n", - " 83\n", + " 84\n", " 0\n", " 0\n", " 0\n", " 0\n", - " 1\n", " \n", " \n", " Mali\n", " 2012\n", " 0\n", - " 28\n", + " 27\n", " 65\n", " 0\n", " 0\n", " 0\n", - " 0\n", - " 1\n", + " 2\n", " \n", " \n", " AG1000G-GQ\n", + " AG1000G-GQ\n", " Equatorial Guinea\n", " 2002\n", " 0\n", @@ -674,10 +962,10 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " AG1000G-GW\n", + " AG1000G-GW\n", " Guinea-Bissau\n", " 2010\n", " 0\n", @@ -687,44 +975,42 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " AG1000G-KE\n", + " AG1000G-KE\n", " Kenya\n", - " 2012\n", - " 10\n", + " 2000\n", " 0\n", " 0\n", + " 19\n", " 0\n", " 0\n", - " 54\n", " 0\n", " 0\n", " \n", " \n", - " 2000\n", + " 2007\n", + " 3\n", " 0\n", " 0\n", - " 19\n", - " 0\n", " 0\n", " 0\n", " 0\n", " 0\n", " \n", " \n", - " 2007\n", - " 3\n", - " 0\n", - " 0\n", + " 2012\n", + " 10\n", " 0\n", " 0\n", " 0\n", " 0\n", + " 54\n", " 0\n", " \n", " \n", + " AG1000G-ML-1\n", " AG1000G-ML-A\n", " Mali\n", " 2014\n", @@ -735,9 +1021,9 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", + " AG1000G-ML-2\n", " AG1000G-ML-B\n", " Mali\n", " 2004\n", @@ -748,10 +1034,10 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " AG1000G-MW\n", + " AG1000G-MW\n", " Malawi\n", " 2015\n", " 41\n", @@ -761,27 +1047,25 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", " AG1000G-MZ\n", + " AG1000G-MZ\n", " Mozambique\n", - " 2004\n", + " 2003\n", " 0\n", " 0\n", - " 71\n", - " 0\n", + " 3\n", " 0\n", " 0\n", " 0\n", " 0\n", " \n", " \n", - " 2003\n", + " 2004\n", " 0\n", " 0\n", - " 3\n", - " 0\n", + " 71\n", " 0\n", " 0\n", " 0\n", @@ -789,6 +1073,7 @@ " \n", " \n", " AG1000G-TZ\n", + " AG1000G-TZ\n", " Tanzania\n", " 2012\n", " 87\n", @@ -798,32 +1083,30 @@ " 0\n", " 0\n", " 0\n", - " 0\n", " \n", " \n", - " 2015\n", - " 137\n", + " 2013\n", + " 1\n", " 0\n", " 32\n", " 0\n", " 0\n", - " 1\n", - " 0\n", + " 10\n", " 0\n", " \n", " \n", - " 2013\n", - " 1\n", + " 2015\n", + " 137\n", " 0\n", " 32\n", " 0\n", " 0\n", - " 10\n", - " 0\n", + " 1\n", " 0\n", " \n", " \n", " AG1000G-UG\n", + " AG1000G-UG\n", " Uganda\n", " 2012\n", " 82\n", @@ -833,163 +1116,255 @@ " 0\n", " 0\n", " 1\n", + " \n", + " \n", + " AG1000G-X\n", + " AG1000G-X\n", + " Lab Cross\n", + " -1\n", + " 0\n", + " 0\n", + " 0\n", " 0\n", + " 0\n", + " 0\n", + " 297\n", " \n", " \n", "\n", "" ], "text/plain": [ - "taxon arabiensis coluzzii \\\n", - "sample_set country year \n", - "AG1000G-AO Angola 2009 0 81 \n", - "AG1000G-BF-A Burkina Faso 2012 0 82 \n", - "AG1000G-BF-B Burkina Faso 2014 3 53 \n", - "AG1000G-BF-C Burkina Faso 2004 0 0 \n", - "AG1000G-CD Democratic Republic of the Congo 2015 0 0 \n", - "AG1000G-CF Central African Republic 1993 0 5 \n", - " 1994 0 13 \n", - "AG1000G-CI Cote d'Ivoire 2012 0 80 \n", - "AG1000G-CM-A Cameroon 2009 0 0 \n", - "AG1000G-CM-B Cameroon 2005 0 7 \n", - "AG1000G-CM-C Cameroon 2013 2 19 \n", - "AG1000G-FR Mayotte 2011 0 0 \n", - "AG1000G-GA-A Gabon 2000 0 0 \n", - "AG1000G-GH Ghana 2012 0 64 \n", - "AG1000G-GM-A Gambia, The 2011 0 0 \n", - "AG1000G-GM-B Gambia, The 2012 0 2 \n", - "AG1000G-GM-C Gambia, The 2012 0 0 \n", - "AG1000G-GN-A Guinea 2012 0 3 \n", - "AG1000G-GN-B Guinea 2012 0 7 \n", - " Mali 2012 0 28 \n", - "AG1000G-GQ Equatorial Guinea 2002 0 0 \n", - "AG1000G-GW Guinea-Bissau 2010 0 0 \n", - "AG1000G-KE Kenya 2012 10 0 \n", - " 2000 0 0 \n", - " 2007 3 0 \n", - "AG1000G-ML-A Mali 2014 0 27 \n", - "AG1000G-ML-B Mali 2004 2 36 \n", - "AG1000G-MW Malawi 2015 41 0 \n", - "AG1000G-MZ Mozambique 2004 0 0 \n", - " 2003 0 0 \n", - "AG1000G-TZ Tanzania 2012 87 0 \n", - " 2015 137 0 \n", - " 2013 1 0 \n", - "AG1000G-UG Uganda 2012 82 0 \n", + "taxon arabiensis \\\n", + "study_id sample_set country year \n", + "AG1000G-AO AG1000G-AO Angola 2009 0 \n", + "AG1000G-BF-1 AG1000G-BF-A Burkina Faso 2012 0 \n", + " AG1000G-BF-B Burkina Faso 2014 3 \n", + "AG1000G-BF-2 AG1000G-BF-C Burkina Faso 2004 0 \n", + "AG1000G-CD AG1000G-CD Democratic Republic of the Congo 2015 0 \n", + "AG1000G-CF AG1000G-CF Central African Republic 1993 0 \n", + " 1994 0 \n", + "AG1000G-CI AG1000G-CI Cote d'Ivoire 2012 0 \n", + "AG1000G-CM-1 AG1000G-CM-A Cameroon 2009 0 \n", + "AG1000G-CM-2 AG1000G-CM-B Cameroon 2005 0 \n", + "AG1000G-CM-3 AG1000G-CM-C Cameroon 2013 2 \n", + "AG1000G-FR AG1000G-FR Mayotte 2011 0 \n", + "AG1000G-GA-1 AG1000G-GA-A Gabon 2000 0 \n", + "AG1000G-GH AG1000G-GH Ghana 2012 0 \n", + "AG1000G-GM-1 AG1000G-GM-A Gambia, The 2011 0 \n", + "AG1000G-GM-2 AG1000G-GM-B Gambia, The 2006 0 \n", + "AG1000G-GM-3 AG1000G-GM-C Gambia, The 2012 0 \n", + "AG1000G-GN-ML AG1000G-GN-A Guinea 2012 0 \n", + " AG1000G-GN-B Guinea 2012 0 \n", + " Mali 2012 0 \n", + "AG1000G-GQ AG1000G-GQ Equatorial Guinea 2002 0 \n", + "AG1000G-GW AG1000G-GW Guinea-Bissau 2010 0 \n", + "AG1000G-KE AG1000G-KE Kenya 2000 0 \n", + " 2007 3 \n", + " 2012 10 \n", + "AG1000G-ML-1 AG1000G-ML-A Mali 2014 0 \n", + "AG1000G-ML-2 AG1000G-ML-B Mali 2004 2 \n", + "AG1000G-MW AG1000G-MW Malawi 2015 41 \n", + "AG1000G-MZ AG1000G-MZ Mozambique 2003 0 \n", + " 2004 0 \n", + "AG1000G-TZ AG1000G-TZ Tanzania 2012 87 \n", + " 2013 1 \n", + " 2015 137 \n", + "AG1000G-UG AG1000G-UG Uganda 2012 82 \n", + "AG1000G-X AG1000G-X Lab Cross -1 0 \n", + "\n", + "taxon coluzzii \\\n", + "study_id sample_set country year \n", + "AG1000G-AO AG1000G-AO Angola 2009 81 \n", + "AG1000G-BF-1 AG1000G-BF-A Burkina Faso 2012 82 \n", + " AG1000G-BF-B Burkina Faso 2014 53 \n", + "AG1000G-BF-2 AG1000G-BF-C Burkina Faso 2004 0 \n", + "AG1000G-CD AG1000G-CD Democratic Republic of the Congo 2015 0 \n", + "AG1000G-CF AG1000G-CF Central African Republic 1993 5 \n", + " 1994 13 \n", + "AG1000G-CI AG1000G-CI Cote d'Ivoire 2012 80 \n", + "AG1000G-CM-1 AG1000G-CM-A Cameroon 2009 0 \n", + "AG1000G-CM-2 AG1000G-CM-B Cameroon 2005 7 \n", + "AG1000G-CM-3 AG1000G-CM-C Cameroon 2013 19 \n", + "AG1000G-FR AG1000G-FR Mayotte 2011 0 \n", + "AG1000G-GA-1 AG1000G-GA-A Gabon 2000 0 \n", + "AG1000G-GH AG1000G-GH Ghana 2012 64 \n", + "AG1000G-GM-1 AG1000G-GM-A Gambia, The 2011 0 \n", + "AG1000G-GM-2 AG1000G-GM-B Gambia, The 2006 0 \n", + "AG1000G-GM-3 AG1000G-GM-C Gambia, The 2012 0 \n", + "AG1000G-GN-ML AG1000G-GN-A Guinea 2012 4 \n", + " AG1000G-GN-B Guinea 2012 7 \n", + " Mali 2012 27 \n", + "AG1000G-GQ AG1000G-GQ Equatorial Guinea 2002 0 \n", + "AG1000G-GW AG1000G-GW Guinea-Bissau 2010 0 \n", + "AG1000G-KE AG1000G-KE Kenya 2000 0 \n", + " 2007 0 \n", + " 2012 0 \n", + "AG1000G-ML-1 AG1000G-ML-A Mali 2014 27 \n", + "AG1000G-ML-2 AG1000G-ML-B Mali 2004 36 \n", + "AG1000G-MW AG1000G-MW Malawi 2015 0 \n", + "AG1000G-MZ AG1000G-MZ Mozambique 2003 0 \n", + " 2004 0 \n", + "AG1000G-TZ AG1000G-TZ Tanzania 2012 0 \n", + " 2013 0 \n", + " 2015 0 \n", + "AG1000G-UG AG1000G-UG Uganda 2012 0 \n", + "AG1000G-X AG1000G-X Lab Cross -1 0 \n", + "\n", + "taxon gambiae \\\n", + "study_id sample_set country year \n", + "AG1000G-AO AG1000G-AO Angola 2009 0 \n", + "AG1000G-BF-1 AG1000G-BF-A Burkina Faso 2012 99 \n", + " AG1000G-BF-B Burkina Faso 2014 46 \n", + "AG1000G-BF-2 AG1000G-BF-C Burkina Faso 2004 13 \n", + "AG1000G-CD AG1000G-CD Democratic Republic of the Congo 2015 76 \n", + "AG1000G-CF AG1000G-CF Central African Republic 1993 2 \n", + " 1994 53 \n", + "AG1000G-CI AG1000G-CI Cote d'Ivoire 2012 0 \n", + "AG1000G-CM-1 AG1000G-CM-A Cameroon 2009 303 \n", + "AG1000G-CM-2 AG1000G-CM-B Cameroon 2005 90 \n", + "AG1000G-CM-3 AG1000G-CM-C Cameroon 2013 23 \n", + "AG1000G-FR AG1000G-FR Mayotte 2011 23 \n", + "AG1000G-GA-1 AG1000G-GA-A Gabon 2000 69 \n", + "AG1000G-GH AG1000G-GH Ghana 2012 36 \n", + "AG1000G-GM-1 AG1000G-GM-A Gambia, The 2011 0 \n", + "AG1000G-GM-2 AG1000G-GM-B Gambia, The 2006 0 \n", + "AG1000G-GM-3 AG1000G-GM-C Gambia, The 2012 2 \n", + "AG1000G-GN-ML AG1000G-GN-A Guinea 2012 41 \n", + " AG1000G-GN-B Guinea 2012 84 \n", + " Mali 2012 65 \n", + "AG1000G-GQ AG1000G-GQ Equatorial Guinea 2002 10 \n", + "AG1000G-GW AG1000G-GW Guinea-Bissau 2010 8 \n", + "AG1000G-KE AG1000G-KE Kenya 2000 19 \n", + " 2007 0 \n", + " 2012 0 \n", + "AG1000G-ML-1 AG1000G-ML-A Mali 2014 33 \n", + "AG1000G-ML-2 AG1000G-ML-B Mali 2004 33 \n", + "AG1000G-MW AG1000G-MW Malawi 2015 0 \n", + "AG1000G-MZ AG1000G-MZ Mozambique 2003 3 \n", + " 2004 71 \n", + "AG1000G-TZ AG1000G-TZ Tanzania 2012 0 \n", + " 2013 32 \n", + " 2015 32 \n", + "AG1000G-UG AG1000G-UG Uganda 2012 207 \n", + "AG1000G-X AG1000G-X Lab Cross -1 0 \n", "\n", - "taxon gambiae gcx1 gcx2 gcx3 \\\n", - "sample_set country year \n", - "AG1000G-AO Angola 2009 0 0 0 0 \n", - "AG1000G-BF-A Burkina Faso 2012 98 0 0 0 \n", - "AG1000G-BF-B Burkina Faso 2014 46 0 0 0 \n", - "AG1000G-BF-C Burkina Faso 2004 13 0 0 0 \n", - "AG1000G-CD Democratic Republic of the Congo 2015 76 0 0 0 \n", - "AG1000G-CF Central African Republic 1993 2 0 0 0 \n", - " 1994 53 0 0 0 \n", - "AG1000G-CI Cote d'Ivoire 2012 0 0 0 0 \n", - "AG1000G-CM-A Cameroon 2009 303 0 0 0 \n", - "AG1000G-CM-B Cameroon 2005 90 0 0 0 \n", - "AG1000G-CM-C Cameroon 2013 23 0 0 0 \n", - "AG1000G-FR Mayotte 2011 23 0 0 0 \n", - "AG1000G-GA-A Gabon 2000 69 0 0 0 \n", - "AG1000G-GH Ghana 2012 36 0 0 0 \n", - "AG1000G-GM-A Gambia, The 2011 0 68 6 0 \n", - "AG1000G-GM-B Gambia, The 2012 0 9 20 0 \n", - "AG1000G-GM-C Gambia, The 2012 2 0 172 0 \n", - "AG1000G-GN-A Guinea 2012 40 0 1 0 \n", - "AG1000G-GN-B Guinea 2012 83 0 0 0 \n", - " Mali 2012 65 0 0 0 \n", - "AG1000G-GQ Equatorial Guinea 2002 10 0 0 0 \n", - "AG1000G-GW Guinea-Bissau 2010 8 93 0 0 \n", - "AG1000G-KE Kenya 2012 0 0 0 54 \n", - " 2000 19 0 0 0 \n", - " 2007 0 0 0 0 \n", - "AG1000G-ML-A Mali 2014 33 0 0 0 \n", - "AG1000G-ML-B Mali 2004 33 0 0 0 \n", - "AG1000G-MW Malawi 2015 0 0 0 0 \n", - "AG1000G-MZ Mozambique 2004 71 0 0 0 \n", - " 2003 3 0 0 0 \n", - "AG1000G-TZ Tanzania 2012 0 0 0 0 \n", - " 2015 32 0 0 1 \n", - " 2013 32 0 0 10 \n", - "AG1000G-UG Uganda 2012 207 0 0 0 \n", + "taxon gcx1 gcx2 \\\n", + "study_id sample_set country year \n", + "AG1000G-AO AG1000G-AO Angola 2009 0 0 \n", + "AG1000G-BF-1 AG1000G-BF-A Burkina Faso 2012 0 0 \n", + " AG1000G-BF-B Burkina Faso 2014 0 0 \n", + "AG1000G-BF-2 AG1000G-BF-C Burkina Faso 2004 0 0 \n", + "AG1000G-CD AG1000G-CD Democratic Republic of the Congo 2015 0 0 \n", + "AG1000G-CF AG1000G-CF Central African Republic 1993 0 0 \n", + " 1994 0 0 \n", + "AG1000G-CI AG1000G-CI Cote d'Ivoire 2012 0 0 \n", + "AG1000G-CM-1 AG1000G-CM-A Cameroon 2009 0 0 \n", + "AG1000G-CM-2 AG1000G-CM-B Cameroon 2005 0 0 \n", + "AG1000G-CM-3 AG1000G-CM-C Cameroon 2013 0 0 \n", + "AG1000G-FR AG1000G-FR Mayotte 2011 0 0 \n", + "AG1000G-GA-1 AG1000G-GA-A Gabon 2000 0 0 \n", + "AG1000G-GH AG1000G-GH Ghana 2012 0 0 \n", + "AG1000G-GM-1 AG1000G-GM-A Gambia, The 2011 68 6 \n", + "AG1000G-GM-2 AG1000G-GM-B Gambia, The 2006 9 22 \n", + "AG1000G-GM-3 AG1000G-GM-C Gambia, The 2012 0 172 \n", + "AG1000G-GN-ML AG1000G-GN-A Guinea 2012 0 0 \n", + " AG1000G-GN-B Guinea 2012 0 0 \n", + " Mali 2012 0 0 \n", + "AG1000G-GQ AG1000G-GQ Equatorial Guinea 2002 0 0 \n", + "AG1000G-GW AG1000G-GW Guinea-Bissau 2010 93 0 \n", + "AG1000G-KE AG1000G-KE Kenya 2000 0 0 \n", + " 2007 0 0 \n", + " 2012 0 0 \n", + "AG1000G-ML-1 AG1000G-ML-A Mali 2014 0 0 \n", + "AG1000G-ML-2 AG1000G-ML-B Mali 2004 0 0 \n", + "AG1000G-MW AG1000G-MW Malawi 2015 0 0 \n", + "AG1000G-MZ AG1000G-MZ Mozambique 2003 0 0 \n", + " 2004 0 0 \n", + "AG1000G-TZ AG1000G-TZ Tanzania 2012 0 0 \n", + " 2013 0 0 \n", + " 2015 0 0 \n", + "AG1000G-UG AG1000G-UG Uganda 2012 0 0 \n", + "AG1000G-X AG1000G-X Lab Cross -1 0 0 \n", "\n", - "taxon intermediate_arabiensis_gambiae \\\n", - "sample_set country year \n", - "AG1000G-AO Angola 2009 0 \n", - "AG1000G-BF-A Burkina Faso 2012 0 \n", - "AG1000G-BF-B Burkina Faso 2014 0 \n", - "AG1000G-BF-C Burkina Faso 2004 0 \n", - "AG1000G-CD Democratic Republic of the Congo 2015 0 \n", - "AG1000G-CF Central African Republic 1993 0 \n", - " 1994 0 \n", - "AG1000G-CI Cote d'Ivoire 2012 0 \n", - "AG1000G-CM-A Cameroon 2009 0 \n", - "AG1000G-CM-B Cameroon 2005 0 \n", - "AG1000G-CM-C Cameroon 2013 0 \n", - "AG1000G-FR Mayotte 2011 0 \n", - "AG1000G-GA-A Gabon 2000 0 \n", - "AG1000G-GH Ghana 2012 0 \n", - "AG1000G-GM-A Gambia, The 2011 0 \n", - "AG1000G-GM-B Gambia, The 2012 0 \n", - "AG1000G-GM-C Gambia, The 2012 0 \n", - "AG1000G-GN-A Guinea 2012 0 \n", - "AG1000G-GN-B Guinea 2012 0 \n", - " Mali 2012 0 \n", - "AG1000G-GQ Equatorial Guinea 2002 0 \n", - "AG1000G-GW Guinea-Bissau 2010 0 \n", - "AG1000G-KE Kenya 2012 0 \n", - " 2000 0 \n", - " 2007 0 \n", - "AG1000G-ML-A Mali 2014 0 \n", - "AG1000G-ML-B Mali 2004 0 \n", - "AG1000G-MW Malawi 2015 0 \n", - "AG1000G-MZ Mozambique 2004 0 \n", - " 2003 0 \n", - "AG1000G-TZ Tanzania 2012 0 \n", - " 2015 0 \n", - " 2013 0 \n", - "AG1000G-UG Uganda 2012 1 \n", + "taxon gcx3 \\\n", + "study_id sample_set country year \n", + "AG1000G-AO AG1000G-AO Angola 2009 0 \n", + "AG1000G-BF-1 AG1000G-BF-A Burkina Faso 2012 0 \n", + " AG1000G-BF-B Burkina Faso 2014 0 \n", + "AG1000G-BF-2 AG1000G-BF-C Burkina Faso 2004 0 \n", + "AG1000G-CD AG1000G-CD Democratic Republic of the Congo 2015 0 \n", + "AG1000G-CF AG1000G-CF Central African Republic 1993 0 \n", + " 1994 0 \n", + "AG1000G-CI AG1000G-CI Cote d'Ivoire 2012 0 \n", + "AG1000G-CM-1 AG1000G-CM-A Cameroon 2009 0 \n", + "AG1000G-CM-2 AG1000G-CM-B Cameroon 2005 0 \n", + "AG1000G-CM-3 AG1000G-CM-C Cameroon 2013 0 \n", + "AG1000G-FR AG1000G-FR Mayotte 2011 0 \n", + "AG1000G-GA-1 AG1000G-GA-A Gabon 2000 0 \n", + "AG1000G-GH AG1000G-GH Ghana 2012 0 \n", + "AG1000G-GM-1 AG1000G-GM-A Gambia, The 2011 0 \n", + "AG1000G-GM-2 AG1000G-GM-B Gambia, The 2006 0 \n", + "AG1000G-GM-3 AG1000G-GM-C Gambia, The 2012 0 \n", + "AG1000G-GN-ML AG1000G-GN-A Guinea 2012 0 \n", + " AG1000G-GN-B Guinea 2012 0 \n", + " Mali 2012 0 \n", + "AG1000G-GQ AG1000G-GQ Equatorial Guinea 2002 0 \n", + "AG1000G-GW AG1000G-GW Guinea-Bissau 2010 0 \n", + "AG1000G-KE AG1000G-KE Kenya 2000 0 \n", + " 2007 0 \n", + " 2012 54 \n", + "AG1000G-ML-1 AG1000G-ML-A Mali 2014 0 \n", + "AG1000G-ML-2 AG1000G-ML-B Mali 2004 0 \n", + "AG1000G-MW AG1000G-MW Malawi 2015 0 \n", + "AG1000G-MZ AG1000G-MZ Mozambique 2003 0 \n", + " 2004 0 \n", + "AG1000G-TZ AG1000G-TZ Tanzania 2012 0 \n", + " 2013 10 \n", + " 2015 1 \n", + "AG1000G-UG AG1000G-UG Uganda 2012 0 \n", + "AG1000G-X AG1000G-X Lab Cross -1 0 \n", "\n", - "taxon intermediate_gambiae_coluzzii \n", - "sample_set country year \n", - "AG1000G-AO Angola 2009 0 \n", - "AG1000G-BF-A Burkina Faso 2012 1 \n", - "AG1000G-BF-B Burkina Faso 2014 0 \n", - "AG1000G-BF-C Burkina Faso 2004 0 \n", - "AG1000G-CD Democratic Republic of the Congo 2015 0 \n", - "AG1000G-CF Central African Republic 1993 0 \n", - " 1994 0 \n", - "AG1000G-CI Cote d'Ivoire 2012 0 \n", - "AG1000G-CM-A Cameroon 2009 0 \n", - "AG1000G-CM-B Cameroon 2005 0 \n", - "AG1000G-CM-C Cameroon 2013 0 \n", - "AG1000G-FR Mayotte 2011 0 \n", - "AG1000G-GA-A Gabon 2000 0 \n", - "AG1000G-GH Ghana 2012 0 \n", - "AG1000G-GM-A Gambia, The 2011 0 \n", - "AG1000G-GM-B Gambia, The 2012 0 \n", - "AG1000G-GM-C Gambia, The 2012 0 \n", - "AG1000G-GN-A Guinea 2012 1 \n", - "AG1000G-GN-B Guinea 2012 1 \n", - " Mali 2012 1 \n", - "AG1000G-GQ Equatorial Guinea 2002 0 \n", - "AG1000G-GW Guinea-Bissau 2010 0 \n", - "AG1000G-KE Kenya 2012 0 \n", - " 2000 0 \n", - " 2007 0 \n", - "AG1000G-ML-A Mali 2014 0 \n", - "AG1000G-ML-B Mali 2004 0 \n", - "AG1000G-MW Malawi 2015 0 \n", - "AG1000G-MZ Mozambique 2004 0 \n", - " 2003 0 \n", - "AG1000G-TZ Tanzania 2012 0 \n", - " 2015 0 \n", - " 2013 0 \n", - "AG1000G-UG Uganda 2012 0 " + "taxon unassigned \n", + "study_id sample_set country year \n", + "AG1000G-AO AG1000G-AO Angola 2009 0 \n", + "AG1000G-BF-1 AG1000G-BF-A Burkina Faso 2012 0 \n", + " AG1000G-BF-B Burkina Faso 2014 0 \n", + "AG1000G-BF-2 AG1000G-BF-C Burkina Faso 2004 0 \n", + "AG1000G-CD AG1000G-CD Democratic Republic of the Congo 2015 0 \n", + "AG1000G-CF AG1000G-CF Central African Republic 1993 0 \n", + " 1994 0 \n", + "AG1000G-CI AG1000G-CI Cote d'Ivoire 2012 0 \n", + "AG1000G-CM-1 AG1000G-CM-A Cameroon 2009 0 \n", + "AG1000G-CM-2 AG1000G-CM-B Cameroon 2005 0 \n", + "AG1000G-CM-3 AG1000G-CM-C Cameroon 2013 0 \n", + "AG1000G-FR AG1000G-FR Mayotte 2011 0 \n", + "AG1000G-GA-1 AG1000G-GA-A Gabon 2000 0 \n", + "AG1000G-GH AG1000G-GH Ghana 2012 0 \n", + "AG1000G-GM-1 AG1000G-GM-A Gambia, The 2011 0 \n", + "AG1000G-GM-2 AG1000G-GM-B Gambia, The 2006 0 \n", + "AG1000G-GM-3 AG1000G-GM-C Gambia, The 2012 0 \n", + "AG1000G-GN-ML AG1000G-GN-A Guinea 2012 0 \n", + " AG1000G-GN-B Guinea 2012 0 \n", + " Mali 2012 2 \n", + "AG1000G-GQ AG1000G-GQ Equatorial Guinea 2002 0 \n", + "AG1000G-GW AG1000G-GW Guinea-Bissau 2010 0 \n", + "AG1000G-KE AG1000G-KE Kenya 2000 0 \n", + " 2007 0 \n", + " 2012 0 \n", + "AG1000G-ML-1 AG1000G-ML-A Mali 2014 0 \n", + "AG1000G-ML-2 AG1000G-ML-B Mali 2004 0 \n", + "AG1000G-MW AG1000G-MW Malawi 2015 0 \n", + "AG1000G-MZ AG1000G-MZ Mozambique 2003 0 \n", + " 2004 0 \n", + "AG1000G-TZ AG1000G-TZ Tanzania 2012 0 \n", + " 2013 0 \n", + " 2015 0 \n", + "AG1000G-UG AG1000G-UG Uganda 2012 1 \n", + "AG1000G-X AG1000G-X Lab Cross -1 297 " ] }, - "execution_count": 4, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -997,7 +1372,7 @@ "source": [ "df_samples = ag3.sample_metadata(sample_sets=\"3.0\")\n", "df_summary = df_samples.pivot_table(\n", - " index=[\"sample_set\", \"country\", \"year\"], \n", + " index=[\"study_id\",\"sample_set\", \"country\", \"year\"], \n", " columns=[\"taxon\"],\n", " values=\"sample_id\", \n", " aggfunc=len,\n",