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go富集气泡图r语言 go富集柱状图r语言

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R语言可视化之ggplot2——KEGG通路富集分析之前分享了如何用ggplot2可视化GO分析的结果 。既然做了GO ， 当然少不了KEGG了 。
同样的，我们从 DAVID 获取KEGG pathway的结果 。
对于KEGG，我比较喜欢做气泡图 ， 这样用两种形式的图结合在一起，效果更丰富更好看一点 。
《R语言实战》自学笔记66-气泡图数据准备
气泡图（bubble plot）：在二维散点图的基础上，用点的大小来代表第三个变量的值 。
symbols()函数来创建气泡图 。该函数可以在指定的(x, y)坐标上绘制圆圈图、方形图、星形图、温度计图和箱线图 。
symbols(x, y, circle=radius)
其中x、y和radius是需要设定的向量 ， 分别表示x、y坐标和圆圈半径 。
你可能想用面积而不是半径来表示第三个变量，那么按照圆圈半径的公式（r = /πA ）变换即可:
symbols(x, y, circle=sqrt(z/pi))
一般来说，统计人员使用R时都倾向于避免用气泡图，原因和避免使用饼图一样：相比对长度的判断，人们对体积/面积的判断通常更困难 。
参考资料：
【R语言】解决GO富集分析绘图，标签重叠问题 前面我给大家详细介绍过
?GO简介及GO富集结果解读
?四种GO富集柱形图、气泡图解读
?GO富集分析四种风格展示结果—柱形图，气泡图
?KEGG富集分析—柱形图，气泡图 ， 通路图
?DAVID GO和KEGG富集分析及结果可视化
也用视频给大家介绍过
?GO和KEGG富集分析视频讲解
最近有粉丝反映说，利用clusterProfiler这个包绘制GO富集分析气泡图和柱形图的时候 ， 发现GO条目的名字都重叠在一起了 。
气泡图
柱形图
这个图别说美观了，简直不忍直视 。经过我的认真研究 ， 发现跟R版本有关 。前面我给大家展示的基本都是R 3.6.3做出来的图 。很多粉丝可能用的都是最新版本的R 4.1.2 。
我们知道R的版本在不停的更新，相应的R包也在不停的更新 。我把绘制气泡图和柱形图相关的函数拿出来认真的研究了一下，终于发现的症结所在 。
dotplot这个函数，多了个 label_format 参数
我们来看看这个参数究竟是干什么用的，看看参数说明
label_format :
a numeric value sets wrap length, alternatively a custom function to format axis labels. by default wraps names longer that 30 characters
原来这个参数默认值是30，当标签的长度大于30个字符就会被折叠，用多行来展示 。既然问题找到了，我们就来调节一下这个参数，把他设置成100，让我们的标签可以一行展示 。
是不是还是原来的配方，还是熟悉的味道
同样的柱形图，我们也能让他恢复原来的容貌 。
关于如何使用R做GO和KEGG富集分析，可参考下文
GO和KEGG富集分析视频讲解
ggplot2绘制Pathway富集分析气泡图Term_NameGeneHitsInSelectedSetAllGenesInSelectedSetGeneHitsInBackgroundAllGenesInBackgroundp-value enrichFactorGeneListInSelectedSetsQvalue
00941 Flavonoid biosynthesis14492 4138573.30E-042.676878842 "[FvH4_2g26480, FvH4_2g05780, FvH4_4g23870, FvH4_5g35170, FvH4_5g14010, FvH4_7g01160, FvH4_3g44420, FvH4_7g20870, FvH4_4g06180, FvH4_5g01170, FvH4_6g28410, FvH4_3g40570, FvH4_5g22390, FvH4_7g25890]"0.04909626
00360 Phenylalanine metabolism14492 4638570.001221701 2.38591375"[FvH4_2g05780, FvH4_4g23870, FvH4_5g35170, FvH4_6g16060, FvH4_4g06180, FvH4_4g25490, FvH4_6g16460, FvH4_6g27650, FvH4_4g09340, FvH4_7g19130, FvH4_3g40570, FvH4_6g26610, FvH4_6g27940, FvH4_6g26600]"0.091016736
00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis 9492 3138570.012547314 2.275963808 "[FvH4_2g05780, FvH4_4g23870, FvH4_5g35170, FvH4_6g28410, FvH4_3g40570, FvH4_5g22390, FvH4_6g26800, FvH4_3g44420, FvH4_4g06180]"0.467387431
00270 Cysteine and methionine metabolism17492 9438570.083418875 1.417769417 "[FvH4_4g21340, FvH4_1g10540, FvH4_4g01140, FvH4_2g02530, FvH4_6g27650, FvH4_1g18690, FvH4_5g05120, FvH4_3g14020, FvH4_6g26610, FvH4_4g13980, FvH4_1g18490, FvH4_6g26600, FvH4_1g21920, FvH4_1g26460, FvH4_2g05040, FvH4_2g41260, FvH4_4g13280]"0.654179598
04120 Ubiquitin mediated proteolysis23492 126 38570.045292621.431007227 "[FvH4_7g29370, FvH4_6g11010, FvH4_6g38720, FvH4_5g03910, FvH4_3g09200, FvH4_6g17370, FvH4_3g39370, FvH4_4g01260, FvH4_2g39250, FvH4_5g30320, FvH4_3g00910, FvH4_5g29350, FvH4_6g35920, FvH4_5g33030, FvH4_1g05910, FvH4_5g22570, FvH4_4g14790, FvH4_1g25030, FvH4_4g17530, FvH4_7g16630, FvH4_6g09540, FvH4_6g10930, FvH4_3g18500]"0.674860033
00260 Glycine, serine and threonine metabolism11492 4938570.04081071.759872242 "[FvH4_1g08890, FvH4_7g07540, FvH4_5g38450, FvH4_2g05310, FvH4_2g22570, FvH4_1g21920, FvH4_2g16830, FvH4_2g36660, FvH4_1g19090, FvH4_4g13290, FvH4_4g25490]"0.675643816
00670 One carbon pool by folate 5492 1838570.069014744 2.177619693 "[FvH4_7g07540, FvH4_5g38450, FvH4_1g00040, FvH4_1g19090, FvH4_4g13290]"0.685546458
03015 mRNA surveillance pathway 20492 114 38570.082844862 1.375338753 "[FvH4_7g29390, FvH4_6g17300, FvH4_5g13570, FvH4_3g29340, FvH4_4g03530, FvH4_2g38640, FvH4_1g18700, FvH4_1g18000, FvH4_2g34040, FvH4_5g33710, FvH4_6g06810, FvH4_5g25490, FvH4_5g03260, FvH4_2g15670, FvH4_4g07000, FvH4_4g36800, FvH4_5g25550, FvH4_2g06580, FvH4_5g05510, FvH4_6g09230]"0.685771358
00603 Glycosphingolipid biosynthesis - globo and isoglobo series3492 938570.096237762 2.613143631 "[FvH4_7g21240, FvH4_6g11740, FvH4_3g04760]"0.71697133
00400 Phenylalanine, tyrosine and tryptophan biosynthesis9492 3738570.038722924 1.906888596 "[FvH4_7g11530, FvH4_6g27650, FvH4_6g26610, FvH4_4g21980, FvH4_6g26600, FvH4_2g22570, FvH4_6g47770, FvH4_5g36810, FvH4_1g20450]"0.721214462
00071 Fatty acid degradation8492 3538570.068800169 1.791869919 "[FvH4_1g26810, FvH4_1g08890, FvH4_5g05130, FvH4_2g14760, FvH4_4g18500, FvH4_1g25230, FvH4_2g37760, FvH4_6g40560]"0.732230372
04712 Circadian rhythm - plant5492 1438570.024734738 2.799796748 "[FvH4_2g29440, FvH4_7g29370, FvH4_1g17250, FvH4_7g01160, FvH4_5g22570]"0.737095202
03410 Base excision repair8492 3438570.059397181.844571975 "[FvH4_4g29150, FvH4_4g36650, FvH4_2g21980, FvH4_6g11530, FvH4_2g39710, FvH4_4g35010, FvH4_2g40160, FvH4_4g35030]"0.737514985
00130 Ubiquinone and other terpenoid-quinone biosynthesis8492 3438570.059397181.844571975 "[FvH4_4g28800, FvH4_4g09340, FvH4_3g40570, FvH4_6g26610, FvH4_6g27940, FvH4_6g26600, FvH4_4g06180, FvH4_6g16460]"0.737514985
00460 Cyanoamino acid metabolism7492 3238570.103957465 1.714875508 "[FvH4_4g26180, FvH4_7g07540, FvH4_5g38450, FvH4_7g05220, FvH4_1g19090, FvH4_4g13290, FvH4_3g43510]"0.737602967
00310 Lysine degradation8492 3038570.030124137 2.090514905 "[FvH4_1g08890, FvH4_5g05130, FvH4_3g23070, FvH4_1g16260, FvH4_1g25230, FvH4_2g36660, FvH4_6g40560, FvH4_3g25420]"0.748082742
00785 Lipoic acid metabolism2492 438570.081725815 3.919715447 "[FvH4_6g44960, FvH4_4g37350]"0.761071655
00601 Glycosphingolipid biosynthesis - lacto and neolacto series2492 438570.081725815 3.919715447 "[FvH4_6g11740, FvH4_3g04760]"0.761071655
00940 Phenylpropanoid biosynthesis26492 149 38570.056260767 1.367954384 "[FvH4_2g05780, FvH4_4g23870, FvH4_5g35170, FvH4_7g32980, FvH4_2g30540, FvH4_2g26620, FvH4_7g05220, FvH4_3g44420, FvH4_6g16060, FvH4_4g06180, FvH4_6g16460, FvH4_3g43510, FvH4_7g19130, FvH4_4g26180, FvH4_6g28410, FvH4_6g27940, FvH4_4g36130, FvH4_3g46010, FvH4_1g16790, FvH4_6g30610, FvH4_4g09340, FvH4_3g15230, FvH4_3g40570, FvH4_5g22390, FvH4_6g27610, FvH4_5g21320]"0.762077663
00450 Selenocompound metabolism 4492 1538570.113762224 2.090514905 "[FvH4_2g38710, FvH4_7g04540, FvH4_6g24170, FvH4_2g41260]"0.770480519
00563 Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 3492 1338570.224775136 1.809099437 "[FvH4_5g04770, FvH4_2g15820, FvH4_1g19740]"0.797416555
03008 Ribosome biogenesis in eukaryotes 6492 3338570.238324783 1.425351072 "[FvH4_1g27070, FvH4_1g17250, FvH4_1g16590, FvH4_2g38700, FvH4_3g27590, FvH4_1g22910]"0.807054378
00860 Porphyrin and chlorophyll metabolism8492 4738570.244407142 1.334371216 "[FvH4_3g20600, FvH4_5g33760, FvH4_7g25640, FvH4_2g27000, FvH4_3g20590, FvH4_1g04700, FvH4_2g23050, FvH4_4g37020]"0.809259204
00053 Ascorbate and aldarate metabolism 8492 4738570.244407142 1.334371216 "[FvH4_1g08890, FvH4_5g05130, FvH4_3g33910, FvH4_6g20720, FvH4_7g08190, FvH4_7g13380, FvH4_1g25230, FvH4_5g20650]"0.809259204
00944 Flavone and flavonol biosynthesis 2492 538570.124932679 3.135772358 "[FvH4_6g17070, FvH4_5g14010]"0.809346486
00040 Pentose and glucuronate interconversions15492 9638570.236599083 1.224911077 "[FvH4_2g26010, FvH4_6g41430, FvH4_6g17310, FvH4_6g17430, FvH4_3g01680, FvH4_5g27090, FvH4_6g53340, FvH4_2g19540, FvH4_5g33570, FvH4_1g00260, FvH4_2g25970, FvH4_7g08190, FvH4_1g26360, FvH4_4g21500, FvH4_1g27720]"0.819843336
03450 Non-homologous end-joining2492 738570.221439565 2.239837398 "[FvH4_4g35010, FvH4_4g35030]"0.824862379
00942 Anthocyanin biosynthesis2492 738570.221439565 2.239837398 "[FvH4_3g19220, FvH4_7g33840]"0.824862379
这是参考以下教程用自己go富集气泡图r语言的数据实现一遍go富集气泡图r语言，
R语言ggplot2画图系列——Pathway富集分析气泡图 - 生信技能树 - Powered by Discuz!;action=printabletid=927
R语言ggplot2绘图教程——Pathway富集分析气泡图 - CSDN博客
转录组不求人系列(十三): GO、KEGG富集个性化作图 当富集分析完成，拿到如下的分析结果后 ， 就可以进行作图了 。
富集分析结果的可视化无非就是柱状图和气泡图，但是公司默认出图实在是太丑，所以还是自己动手修改修改 。
一、常规柱状图（ggplot2）
横轴为gene counts，或者用-logP也行，填充相应的用P值或者gene counts 。ggplot画图的好处就是可以进行很多调整 。
二、常规气泡图（ggplot2）
气泡图与柱状图如出一辙，只是在展示方式上出现了差别 。一个用geom_bar()函数，气泡图类似于散点图用geom_point()函数 。
三、上下调同时展示（ggplot2）
很多时候研究者拿到差异基因后 ， 上下调基因是分别富集的，在展示上需要同时体现二者，我们之前提到metascape可以做到： 转录组不求人系列(十二): Cell文章最喜欢用的差异基因GO、KEGG富集分析工具 ，除此之外 ， 之前讲过的气泡图也可以展现多组的结果： 复现《nature communications》图表（四）：ggplot画多组富集气泡图。这里我们继续提供一种bar图的展示方式 。将down的数值调整为负，做一列分组，就可以展示了 。
当然了，以上所说的可视化还是比较常规，在基础上可以自己做调整 。也有一些文章总是标新立意，有很多奇特的展现方式，我们会在之后的系列中讲解 。
【go富集气泡图r语言 go富集柱状图r语言】go富集气泡图r语言的介绍就聊到这里吧，感谢你花时间阅读本站内容，更多关于go富集柱状图r语言、go富集气泡图r语言的信息别忘了在本站进行查找喔 。

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