跟着Nature Communications学作图：R语言ggplot2箱线图/抖动散点图展示多物种基因组大小和TE含量

docs/2023-09/跟着Nature_Communications学作图_R语言ggplot2箱线图_抖动散点图展示多物种基因组大小和TE含量.md

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+---
+title: "跟着Nature Communications学作图：R语言ggplot2箱线图/抖动散点图展示多物种基因组大小和TE含量"
+date: 2023-09-09T15:31:24Z
+draft: ["false"]
+tags: [
+  "fetched",
+  "小明的数据分析笔记本"
+]
+categories: ["Acdemic"]
+---
+跟着Nature Communications学作图：R语言ggplot2箱线图/抖动散点图展示多物种基因组大小和TE含量 by 小明的数据分析笔记本
+------
+<div><section data-tool="mdnice编辑器" data-website="https://www.mdnice.com" data-mpa-powered-by="yiban.io"><h2 data-tool="mdnice编辑器"><span></span><span>论文</span><span></span><span> </span></h2><blockquote data-tool="mdnice编辑器"><p>Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits</p></blockquote><p data-tool="mdnice编辑器">https://www.nature.com/articles/s41467-020-18795-w</p><p data-tool="mdnice编辑器"><code>s41467-020-18795-w.pdf</code></p><p data-tool="mdnice编辑器">这个是是有读者在公众号后台留言问到</p><p data-tool="mdnice编辑器"><img data-ratio="0.43665436654366546" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIpVibxf9FJZ99ejWos6zndoD8l83BDkrXiakyGvdIAeiaVq8U6jN54PmMg/640?wx_fmt=png" data-type="png" data-w="813" src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIpVibxf9FJZ99ejWos6zndoD8l83BDkrXiakyGvdIAeiaVq8U6jN54PmMg/640?wx_fmt=png">我把论文找来看了一下，论文对应的图大部分都有数据，我们可以试着复现其中的图，先从最简单的的开始，论文中的Figure2是箱线图加抖动散点图，论文的配色也很好看，可以保留作为自己配色备选</p><h2 data-tool="mdnice编辑器"><span></span><span>部分示例数据截图</span><span></span><span> </span></h2><figure data-tool="mdnice编辑器"><img data-ratio="0.1699810606060606" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIBibicrXpuickGXyhSUsib2z87icN7Nibibe5znOTOUiaa1ItUibXG2LE7eSUPYQ/640?wx_fmt=png" data-type="png" data-w="2112" src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIBibicrXpuickGXyhSUsib2z87icN7Nibibe5znOTOUiaa1ItUibXG2LE7eSUPYQ/640?wx_fmt=png"><figcaption>image.png</figcaption></figure><p data-tool="mdnice编辑器">首先是读取数据</p><pre data-tool="mdnice编辑器"><span></span><code>library(tidyverse)<br><br>dat&lt;-read_delim(<span>"data/20230909/Source Data/Source_Data_figure_1a.csv"</span>,<br>           delim = <span>","</span>)<br><br>colnames(dat)<br><br><br>dat %&gt;% <br>  pull(Ecology) %&gt;% <br>  table()<br></code></pre><p data-tool="mdnice编辑器">左侧的图展示基因组大小，代码如下</p><pre data-tool="mdnice编辑器"><span></span><code>ggplot(data=dat %&gt;% <br>         filter(Ecology!=<span>"Yeast"</span>&amp;Ecology!=<span>"Parasite"</span>) %&gt;% <br>       mutate(Ecology=factor(Ecology,levels = c(<span>"Wood decayer"</span>,<br>                                                <span>"Endophyte"</span>,<br>                                                <span>"Arbuscular mycorrhizae"</span>,<br>                                                <span>"Orchid mycorrhizae"</span>,<br>                                                <span>"Ericoid mycorrhizae"</span>,<br>                                                <span>"Pathogen"</span>,<br>                                                <span>"Saprotroph"</span>,<br>                                                <span>"Ectomycorrhizae"</span>))),<br>       aes(x=Genome.size,y=Ecology))+<br>  geom_boxplot(color=<span>"gray"</span>)+<br>  geom_jitter(aes(color=Ecology),<br>              size=5,<br>              show.legend = FALSE,<br>              alpha=0.5)+<br>  scale_color_manual(values = c(<span>"#f1a2c9"</span>,<span>"#b6b3b3"</span>,<span>"#a8e3ea"</span>,<br>                                <span>"#fde05f"</span>,<span>"#f49b40"</span>,<br>                                <span>"#7ac84e"</span>,<span>"#73a1cb"</span>,<span>"#e15e53"</span>))+<br>  scale_x_continuous(limits = c(0,150000000),<br>                     labels = <span>function</span>(x){x/1000000})+<br>  theme_bw()+<br>  theme(panel.border = element_blank(),<br>        axis.ticks = element_blank())+<br>  labs(x=NULL,y=NULL,title = <span>"Genomes (Mbp)"</span>)<br></code></pre><figure data-tool="mdnice编辑器"><img data-ratio="0.6509695290858726" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIrHh3z3Xj6AEuNXgbjstao1bngEPWTzOfwCCiauw9haI94RlVMFfMQhw/640?wx_fmt=png" data-type="png" data-w="722" src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIrHh3z3Xj6AEuNXgbjstao1bngEPWTzOfwCCiauw9haI94RlVMFfMQhw/640?wx_fmt=png"><figcaption>image.png</figcaption></figure><p data-tool="mdnice编辑器">右侧的图代码基本一样</p><pre data-tool="mdnice编辑器"><span></span><code>ggplot(data=dat %&gt;% <br>         filter(Ecology!=<span>"Yeast"</span>&amp;Ecology!=<span>"Parasite"</span>) %&gt;% <br>         mutate(Ecology=factor(Ecology,levels = c(<span>"Wood decayer"</span>,<br>                                                  <span>"Endophyte"</span>,<br>                                                  <span>"Arbuscular mycorrhizae"</span>,<br>                                                  <span>"Orchid mycorrhizae"</span>,<br>                                                  <span>"Ericoid mycorrhizae"</span>,<br>                                                  <span>"Pathogen"</span>,<br>                                                  <span>"Saprotroph"</span>,<br>                                                  <span>"Ectomycorrhizae"</span>))),<br>       aes(x=TE.CoverageTotal,y=Ecology))+<br>  geom_boxplot(color=<span>"gray"</span>)+<br>  geom_jitter(aes(color=Ecology),<br>              size=5,<br>              show.legend = FALSE,<br>              alpha=0.5)+<br>  scale_color_manual(values = c(<span>"#f1a2c9"</span>,<span>"#b6b3b3"</span>,<span>"#a8e3ea"</span>,<br>                                <span>"#fde05f"</span>,<span>"#f49b40"</span>,<br>                                <span>"#7ac84e"</span>,<span>"#73a1cb"</span>,<span>"#e15e53"</span>))+<br>  scale_x_continuous(limits = c(0,100))+<br>  theme_bw()+<br>  theme(panel.border = element_blank(),<br>        axis.ticks = element_blank(),<br>        axis.text.y = element_blank())+<br>  labs(x=NULL,y=NULL,title = <span>"Repeat element coverage (%)"</span>)<br></code></pre><figure data-tool="mdnice编辑器"><img data-ratio="0.6675938803894298" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIahKeXCJV12zcUY0KDVFhEXjpLoFtxYHiaLdrfibn107MZSABQuUlBDAg/640?wx_fmt=png" data-type="png" data-w="719" src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIahKeXCJV12zcUY0KDVFhEXjpLoFtxYHiaLdrfibn107MZSABQuUlBDAg/640?wx_fmt=png"><figcaption>image.png</figcaption></figure><p data-tool="mdnice编辑器">最后是拼图</p><pre data-tool="mdnice编辑器"><span></span><code>library(patchwork)<br><br>p1+p2<br></code></pre><figure data-tool="mdnice编辑器"><img data-ratio="0.4225" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIsvGKWhCWj6g5b166ibyvzDbAOzlMmFV4QibCn8QKjuJuHibfxKXAK5JNg/640?wx_fmt=png" data-type="png" data-w="2000" src="https://mmbiz.qpic.cn/sz_mmbiz_png/t1wZDoUyFk5WrSg9QGmRgwyickib5hxGbIsvGKWhCWj6g5b166ibyvzDbAOzlMmFV4QibCn8QKjuJuHibfxKXAK5JNg/640?wx_fmt=png"><figcaption>image.png</figcaption></figure><blockquote data-tool="mdnice编辑器"><p>示例数据可以到论文中下载，代码可以在推文中复制，或者给推文打赏一元获取我整理好的数据和代码</p></blockquote><p data-tool="mdnice编辑器">欢迎大家关注我的公众号</p><p data-tool="mdnice编辑器"><strong>小明的数据分析笔记本</strong></p><section><mp-common-profile data-pluginname="mpprofile" data-id="MzI3NzQ3MTcxMg==" data-headimg="http://mmbiz.qpic.cn/mmbiz_png/t1wZDoUyFk5t1sOnM0iabvBhnfIj5YpyqrMib0E1MGCd9ibcYxaOPZd0GWhQBDvK2BPEwsicQxd6y5MHLfphnwHnow/0?wx_fmt=png" data-nickname="小明的数据分析笔记本" data-alias="" data-signature="分享R语言和python在生物信息领域做数据分析和数据可视化的简单小例子；偶尔会分享一些组学数据处理相关的内容" data-from="0" data-is_biz_ban="0"></mp-common-profile></section><p data-tool="mdnice编辑器"></p><blockquote data-tool="mdnice编辑器"><p>小明的数据分析笔记本 公众号 主要分享：1、R语言和python做数据分析和数据可视化的简单小例子；2、园艺植物相关转录组学、基因组学、群体遗传学文献阅读笔记；3、生物信息学入门学习资料及自己的学习笔记！</p></blockquote></section><p><br></p><p><mp-style-type data-value="3"></mp-style-type></p></div>  
+<hr>
+<a href="https://mp.weixin.qq.com/s/8kk04B3ptyhDLRhcdIIf0g",target="_blank" rel="noopener noreferrer">原文链接</a>