{"id":380,"date":"2020-04-26T16:34:00","date_gmt":"2020-04-26T08:34:00","guid":{"rendered":"https:\/\/www.next-bioinfo.tw\/?p=380"},"modified":"2023-11-14T16:47:20","modified_gmt":"2023-11-14T08:47:20","slug":"%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91%e4%bd%bf%e7%94%a8bioinfokit%e7%b9%aa%e8%a3%bd%e7%81%ab%e5%b1%b1%e5%9c%96volcano-plot","status":"publish","type":"post","link":"https:\/\/www.next-bioinfo.tw\/en\/2020\/04\/%e3%80%90ngs-%e6%ac%a1%e4%b8%96%e4%bb%a3%e5%9f%ba%e5%9b%a0%e9%ab%94%e8%b3%87%e6%96%99%e7%a7%91%e5%ad%b8%e3%80%91%e4%bd%bf%e7%94%a8bioinfokit%e7%b9%aa%e8%a3%bd%e7%81%ab%e5%b1%b1%e5%9c%96volcano-plot\/","title":{"rendered":"\u3010NGS with Data Science\u3011Use bioinfokit to make a volcano plot"},"content":{"rendered":"

In this article, I will explain how to use Python to draw a Volcano plot. The Volcano plot was a standard tool for illustrating the differential analysis of gene expression analysis during the downstream of quantitative analysis, which was a special type of scatter plot. The x-axis of the Volcano plot was the log2 Fold change of two conditions, and the y-axis was the negative value of the negative logarithm base 10 of the p-value. Each data point represents a gene or other biological feature being tested. In RNA-Seq, each data point would be the genes.<\/p>\n\n\n\n

\u9019\u88e1\u4ecb\u7d39\u4f7f\u7528Python\u7684\u5957\u4ef6bioinfokit\u4f86\u7e6a\u88fd\u706b\u5c71\u5716\uff0c\u9996\u5148\u6211\u5011\u9700\u8981\u4e0b\u8f09\u7bc4\u4f8b\u8cc7\u6599\u4ee5\u53ca\u5b89\u88ddbioinfokit :<\/p>\n\n\n\n

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pip<\/span> <\/span>install<\/span> <\/span>bioinfokit<\/span><\/span>\n<\/span>\nwget<\/span> <\/span>https:\/\/zenodo.org\/record\/2529117\/files\/limma-voom_luminalpregnant-luminallactate<\/span><\/span>\nwget<\/span> <\/span>https:\/\/zenodo.org\/record\/2529117\/files\/volcano_genes<\/span><\/span><\/code><\/pre><\/div>\n\n\n\n
\u7a0d\u5fae\u770b\u4e00\u4e0b\u8cc7\u6599\u7684\u60c5\u6cc1<\/p>\n\n\n\n
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head<\/span> <\/span>limma-voom_luminalpregnant-luminallactate<\/span><\/span><\/code><\/pre><\/div>\n\n\n\n
\u8f38\u51fa\uff1a<\/p>\n\n\n\n
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ENTREZID<\/span>\t<\/span>SYMBOL<\/span>\t<\/span>GENENAME<\/span>\t<\/span>logFC<\/span>\t<\/span>AveExpr<\/span>\t<\/span>t<\/span>\t<\/span>P.Value<\/span>\t<\/span>adj.P.Val<\/span><\/span>\n12992<\/span>\t<\/span>Csn1s2b<\/span>\t<\/span>casein<\/span> <\/span>alpha<\/span> <\/span>s2-like<\/span> <\/span>B<\/span>\t<\/span>-8.603611114762<\/span>\t<\/span>3.56295004142591<\/span>\t<\/span>-43.7964980711435<\/span>\t<\/span>3.83064977005569<\/span>e-15<\/span>\t<\/span>6.05395889659601<\/span>e-11<\/span><\/span>\n13358<\/span>\t<\/span>Slc25a1<\/span>\t<\/span>solute<\/span> <\/span>carrier<\/span> <\/span>family<\/span> <\/span>25<\/span> (mitochondrial <\/span>carrier,<\/span> <\/span>citrate<\/span> <\/span>transporter<\/span>), member 1\t-4.12417532129173\t5.77969894403042\t-29.9078492752674\t1.75859473379618e-13\t1.38964155864574e-09<\/span><\/span>\n11941<\/span>\t<\/span>Atp2b2<\/span>\t<\/span>ATPase,<\/span> <\/span>Ca++<\/span> <\/span>transporting,<\/span> <\/span>plasma<\/span> <\/span>membrane<\/span> <\/span>2<\/span>\t<\/span>-7.38698638678659<\/span>\t<\/span>1.28214314739647<\/span>\t<\/span>-27.8194991746381<\/span>\t<\/span>4.83636254056037<\/span>e-13<\/span>\t<\/span>2.43279979019347<\/span>e-09<\/span><\/span>\n20531<\/span>\t<\/span>Slc34a2<\/span>\t<\/span>solute<\/span> <\/span>carrier<\/span> <\/span>family<\/span> <\/span>34<\/span> (sodium <\/span>phosphate<\/span>), member 2\t-4.17781242057656\t4.27862903538987\t-27.0727230566646\t6.15742796809282e-13\t2.43279979019347e-09<\/span><\/span>\n100705<\/span>\t<\/span>Acacb<\/span>\t<\/span>acetyl-Coenzyme<\/span> <\/span>A<\/span> <\/span>carboxylase<\/span> <\/span>beta<\/span>\t<\/span>-4.3143199499725<\/span>\t<\/span>4.4409137064501<\/span>\t<\/span>-25.2235657685746<\/span>\t<\/span>1.4999774593805<\/span>e-12<\/span>\t<\/span>4.74112875360987<\/span>e-09<\/span><\/span>\n13645<\/span>\t<\/span>Egf<\/span>\t<\/span>epidermal<\/span> <\/span>growth<\/span> <\/span>factor<\/span>\t<\/span>-5.36266382024579<\/span>\t<\/span>0.73590465313728<\/span>\t<\/span>-24.5993025952199<\/span>\t<\/span>2.11624444834827<\/span>e-12<\/span>\t<\/span>5.57418787694935<\/span>e-09<\/span><\/span>\n230810<\/span>\t<\/span>Slc30a2<\/span>\t<\/span>solute<\/span> <\/span>carrier<\/span> <\/span>family<\/span> <\/span>30<\/span> (zinc <\/span>transporter<\/span>), member 2\t-3.20311813582619\t2.69581147606106\t-23.80427759327\t3.02466813499713e-12\t6.82883645792781e-09<\/span><\/span>\n68801<\/span>\t<\/span>Elovl5<\/span>\t<\/span>ELOVL<\/span> <\/span>family<\/span> <\/span>member<\/span> <\/span>5<\/span>,<\/span> <\/span>elongation<\/span> <\/span>of<\/span> <\/span>long<\/span> <\/span>chain<\/span> <\/span>fatty<\/span> <\/span>acids<\/span> (yeast)\t-2.86330403668687\t6.45520453127796\t-22.3535751591657\t6.5987442593808e-12\t1.30358192844068e-08<\/span><\/span>\n19659<\/span>\t<\/span>Rbp1<\/span>\t<\/span>retinol<\/span> <\/span>binding<\/span> <\/span>protein<\/span> <\/span>1<\/span>,<\/span> <\/span>cellular<\/span>\t<\/span>5.44304402150002<\/span>\t<\/span>6.10703318183881<\/span>\t<\/span>21.0523576693295<\/span>\t<\/span>1.47914323855668<\/span>e-11<\/span>\t<\/span>2.36474559807046<\/span>e-08<\/span><\/span>\n<\/span><\/code><\/pre><\/div>\n\n\n\n
limma-voom_luminalpregnant-luminallactate\u662f\u4e00\u500btsv\u683c\u5f0f\u7684\u4e0b\u6e38\u5206\u6790\u7d50\u679c\u3002\u7e31\u5411\u662f\u57fa\u56e0\uff0c\u6a6b\u5411\u5247\u662f\u6bcf\u500b\u57fa\u56e0\u7684\u8b8a\u5316\u91cf\uff08\u9019\u500b\u6848\u4f8b\u662flogFC\uff09\uff0c\u4ee5\u53caP\u503c\u548c\u6821\u6b63\u5f8cP\u503c\uff08adj.P.Val\uff09<\/p>\n\n\n\n
\u518d\u770b\u4e00\u4e0bvolcano_genes<\/p>\n\n\n\n
<\/path><\/path><\/svg><\/span>
head<\/span> <\/span>volcano_genes<\/span><\/span><\/code><\/pre><\/div>\n\n\n\n
<\/path><\/path><\/svg><\/span>
GeneID<\/span><\/span>\nMcl1<\/span><\/span>\nHbegf<\/span><\/span>\nTgfb2<\/span><\/span>\nCxcl16<\/span><\/span>\nCsf1<\/span><\/span>\nPdgfb<\/span><\/span>\nEdn1<\/span><\/span>\nLif<\/span><\/span>\nKitl<\/span><\/span>\n<\/span><\/code><\/pre><\/div>\n\n\n\n
\u5b83\u662f\u7b49\u4e00\u4e0b\u8981\u6a19\u8a3b\u4e0a\u540d\u7a31\u7684\u5019\u9078\u57fa\u56e0\u540d\u7a31\u7684\u5217\u8868<\/p>\n\n\n\n
\u63a5\u8457\u6211\u5011\u4f7f\u7528pandas\u628atsv\u8b80\u6210dataframe\uff0c\u4e26\u50b3\u5165visuz.GeneExpression.volcano\u9019\u500b\u51fd\u5f0f\u5c31\u53ef\u4ee5\u4e86<\/p>\n\n\n\n
<\/path><\/path><\/svg><\/span>
from<\/span> bioinfokit <\/span>import<\/span> analys<\/span>,<\/span> visuz<\/span><\/span>\nimport<\/span> pandas <\/span>as<\/span> pd<\/span><\/span>\nimport<\/span> matplotlib<\/span>.<\/span>pyplot <\/span>as<\/span> plt<\/span><\/span>\ndf <\/span>=<\/span> pd<\/span>.<\/span>read_csv<\/span>(<\/span>"<\/span>limma-voom_luminalpregnant-luminallactat<\/span>"<\/span>,<\/span> <\/span>sep<\/span>=<\/span>'<\/span>\\t<\/span>'<\/span>)<\/span><\/span>\n<\/span>\nwith<\/span> <\/span>open<\/span>(<\/span>'<\/span>volcano_genes<\/span>'<\/span>)<\/span> <\/span>as<\/span> f<\/span>:<\/span><\/span>\n    genes <\/span>=<\/span> f<\/span>.<\/span>read<\/span>().<\/span>splitlines<\/span>()<\/span><\/span>\n<\/span>\n<\/span>\ndf<\/span>.<\/span>dropna<\/span>(<\/span>inplace<\/span>=True<\/span>)<\/span><\/span>\nvisuz<\/span>.<\/span>GeneExpression<\/span>.<\/span>volcano<\/span>(<\/span>df<\/span>=<\/span>df<\/span>,<\/span> <\/span>lfc<\/span>=<\/span>'<\/span>logFC<\/span>'<\/span>,<\/span> <\/span>pv<\/span>=<\/span>'<\/span>adj.P.Val<\/span>'<\/span>,<\/span> <\/span>lfc_thr<\/span>=<\/span>(<\/span>1<\/span>,<\/span> <\/span>1<\/span>),<\/span> <\/span>sign_line<\/span>=True<\/span>,<\/span> <\/span>plotlegend<\/span>=True<\/span>,<\/span> <\/span>legendpos<\/span>=<\/span>'<\/span>upper right<\/span>'<\/span>,<\/span> <\/span>legendanchor<\/span>=<\/span>(<\/span><\/span>\n    <\/span>1.46<\/span>,<\/span> <\/span>1<\/span>),<\/span> <\/span>dotsize<\/span>=<\/span>0.1<\/span>,<\/span> <\/span>gfont<\/span>=<\/span>7<\/span>,<\/span> <\/span>xlm<\/span>=<\/span>(<\/span>-<\/span>10.0<\/span>,<\/span> <\/span>10.0<\/span>,<\/span> <\/span>1<\/span>),<\/span> <\/span>pv_thr<\/span>=<\/span>(<\/span>0.05<\/span>,<\/span> <\/span>0.05<\/span>),<\/span> <\/span>genenames<\/span>=<\/span>tuple<\/span>(<\/span>genes<\/span>),<\/span> <\/span>geneid<\/span>=<\/span>"<\/span>SYMBOL<\/span>"<\/span>)<\/span><\/span>\n<\/span><\/code><\/pre><\/div>\n\n\n\n
\u57f7\u884c\u4e4b\u5f8c\u6703\u5728\u7a0b\u5f0f\u5f97\u5f97\u76ee\u9304\u4e0b\u8f38\u51fa\u5716\u6a94<\/p>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\u4ee5\u4e0a\u5c31\u662f\u7e6a\u88fd\u706b\u5c71\u5716\u7684\u4ecb\u7d39\u3002<\/p>","protected":false},"excerpt":{"rendered":"
\u9019\u88e1\u4ecb\u7d39\u5982\u4f55\u7528\u73fe\u6210\u7684\u5957\u4ef6\u5feb\u901f\u7e6a\u88fd\u706b\u5c71\u5716\uff08Volcano plot\uff09\u3002\u5728\u505a\u57fa\u56e0\u9ad4\u91cf\u5316\u5206\u6790\u7684\u4e0b\u6e38\uff0c\u5e38\u898b\u9700\u8981\u88fd\u4f5c\u5dee\u7570 […]<\/p>","protected":false},"author":1,"featured_media":264,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_mi_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"site-container-style":"default","site-container-layout":"default","site-sidebar-layout":"default","site-transparent-header":"default","disable-article-header":"default","disable-site-header":"default","disable-site-footer":"default","disable-content-area-spacing":"default","footnotes":""},"categories":[2],"tags":[48,49,45,47,46],"_links":{"self":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/380"}],"collection":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/comments?post=380"}],"version-history":[{"count":1,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/380\/revisions"}],"predecessor-version":[{"id":382,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/posts\/380\/revisions\/382"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media\/264"}],"wp:attachment":[{"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/media?parent=380"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/categories?post=380"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.next-bioinfo.tw\/en\/wp-json\/wp\/v2\/tags?post=380"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}