R語言可視化之ggplot2——KEGG通路富集分析

之前分享了如何用ggplot2可視化GO分析的結(jié)果。既然做了GO，當(dāng)然少不了KEGG了。

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同樣的，我們從 DAVID 獲取KEGG pathway的結(jié)果。

對(duì)于KEGG，我比較喜歡做氣泡圖，這樣用兩種形式的圖結(jié)合在一起，效果更豐富更好看一點(diǎn)。

ggplot2繪制Pathway富集分析氣泡圖

Term_Name GeneHitsInSelectedSet AllGenesInSelectedSet GeneHitsInBackground AllGenesInBackground p-value enrichFactor GeneListInSelectedSets Qvalue

00941 Flavonoid biosynthesis 14 492 41 3857 3.30E-04 2.676878842 "[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 metabolism 14 492 46 3857 0.001221701 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 9 492 31 3857 0.012547314 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 metabolism 17 492 94 3857 0.083418875 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 proteolysis 23 492 126 3857 0.04529262 1.431007227 "[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 metabolism 11 492 49 3857 0.0408107 1.759872242 "[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 5 492 18 3857 0.069014744 2.177619693 "[FvH4_7g07540, FvH4_5g38450, FvH4_1g00040, FvH4_1g19090, FvH4_4g13290]" 0.685546458

03015 mRNA surveillance pathway 20 492 114 3857 0.082844862 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 series 3 492 9 3857 0.096237762 2.613143631 "[FvH4_7g21240, FvH4_6g11740, FvH4_3g04760]" 0.71697133

00400 Phenylalanine, tyrosine and tryptophan biosynthesis 9 492 37 3857 0.038722924 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 degradation 8 492 35 3857 0.068800169 1.791869919 "[FvH4_1g26810, FvH4_1g08890, FvH4_5g05130, FvH4_2g14760, FvH4_4g18500, FvH4_1g25230, FvH4_2g37760, FvH4_6g40560]" 0.732230372

04712 Circadian rhythm - plant 5 492 14 3857 0.024734738 2.799796748 "[FvH4_2g29440, FvH4_7g29370, FvH4_1g17250, FvH4_7g01160, FvH4_5g22570]" 0.737095202

03410 Base excision repair 8 492 34 3857 0.05939718 1.844571975 "[FvH4_4g29150, FvH4_4g36650, FvH4_2g21980, FvH4_6g11530, FvH4_2g39710, FvH4_4g35010, FvH4_2g40160, FvH4_4g35030]" 0.737514985

00130 Ubiquinone and other terpenoid-quinone biosynthesis 8 492 34 3857 0.05939718 1.844571975 "[FvH4_4g28800, FvH4_4g09340, FvH4_3g40570, FvH4_6g26610, FvH4_6g27940, FvH4_6g26600, FvH4_4g06180, FvH4_6g16460]" 0.737514985

00460 Cyanoamino acid metabolism 7 492 32 3857 0.103957465 1.714875508 "[FvH4_4g26180, FvH4_7g07540, FvH4_5g38450, FvH4_7g05220, FvH4_1g19090, FvH4_4g13290, FvH4_3g43510]" 0.737602967

00310 Lysine degradation 8 492 30 3857 0.030124137 2.090514905 "[FvH4_1g08890, FvH4_5g05130, FvH4_3g23070, FvH4_1g16260, FvH4_1g25230, FvH4_2g36660, FvH4_6g40560, FvH4_3g25420]" 0.748082742

00785 Lipoic acid metabolism 2 492 4 3857 0.081725815 3.919715447 "[FvH4_6g44960, FvH4_4g37350]" 0.761071655

00601 Glycosphingolipid biosynthesis - lacto and neolacto series 2 492 4 3857 0.081725815 3.919715447 "[FvH4_6g11740, FvH4_3g04760]" 0.761071655

00940 Phenylpropanoid biosynthesis 26 492 149 3857 0.056260767 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 4 492 15 3857 0.113762224 2.090514905 "[FvH4_2g38710, FvH4_7g04540, FvH4_6g24170, FvH4_2g41260]" 0.770480519

00563 Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 3 492 13 3857 0.224775136 1.809099437 "[FvH4_5g04770, FvH4_2g15820, FvH4_1g19740]" 0.797416555

03008 Ribosome biogenesis in eukaryotes 6 492 33 3857 0.238324783 1.425351072 "[FvH4_1g27070, FvH4_1g17250, FvH4_1g16590, FvH4_2g38700, FvH4_3g27590, FvH4_1g22910]" 0.807054378

00860 Porphyrin and chlorophyll metabolism 8 492 47 3857 0.244407142 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 8 492 47 3857 0.244407142 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 2 492 5 3857 0.124932679 3.135772358 "[FvH4_6g17070, FvH4_5g14010]" 0.809346486

00040 Pentose and glucuronate interconversions 15 492 96 3857 0.236599083 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-joining 2 492 7 3857 0.221439565 2.239837398 "[FvH4_4g35010, FvH4_4g35030]" 0.824862379

00942 Anthocyanin biosynthesis 2 492 7 3857 0.221439565 2.239837398 "[FvH4_3g19220, FvH4_7g33840]" 0.824862379

這是參考以下教程用自己的數(shù)據(jù)實(shí)現(xiàn)一遍，

R語言ggplot2畫圖系列——Pathway富集分析氣泡圖 - 生信技能樹 - Powered by Discuz! ;action=printabletid=927

R語言ggplot2繪圖教程——Pathway富集分析氣泡圖 - CSDN博客

《R語言實(shí)戰(zhàn)》自學(xué)筆記66-氣泡圖

數(shù)據(jù)準(zhǔn)備

氣泡圖（bubble plot）：在二維散點(diǎn)圖的基礎(chǔ)上，用點(diǎn)的大小來代表第三個(gè)變量的值。

symbols()函數(shù)來創(chuàng)建氣泡圖。該函數(shù)可以在指定的(x, y)坐標(biāo)上繪制圓圈圖、方形圖、星形圖、溫度計(jì)圖和箱線圖。

symbols(x, y, circle=radius)

其中x、y和radius是需要設(shè)定的向量，分別表示x、y坐標(biāo)和圓圈半徑。

你可能想用面積而不是半徑來表示第三個(gè)變量，那么按照?qǐng)A圈半徑的公式（r = /πA ）變換即可:

symbols(x, y, circle=sqrt(z/pi))

一般來說，統(tǒng)計(jì)人員使用R時(shí)都傾向于避免用氣泡圖，原因和避免使用餅圖一樣：相比對(duì)長(zhǎng)度的判斷，人們對(duì)體積/面積的判斷通常更困難。

參考資料：

【R語言】解決GO富集分析繪圖，標(biāo)簽重疊問題

前面我給大家詳細(xì)介紹過

?GO簡(jiǎn)介及GO富集結(jié)果解讀

?四種GO富集柱形圖、氣泡圖解讀

?GO富集分析四種風(fēng)格展示結(jié)果—柱形圖，氣泡圖

?KEGG富集分析—柱形圖，氣泡圖，通路圖

? DAVID GO和KEGG富集分析及結(jié)果可視化

也用視頻給大家介紹過

? GO和KEGG富集分析視頻講解

最近有粉絲反映說，利用clusterProfiler這個(gè)包繪制GO富集分析氣泡圖和柱形圖的時(shí)候，發(fā)現(xiàn)GO條目的名字都重疊在一起了。

氣泡圖

柱形圖

這個(gè)圖別說美觀了，簡(jiǎn)直不忍直視。經(jīng)過我的認(rèn)真研究，發(fā)現(xiàn)跟R版本有關(guān)。前面我給大家展示的基本都是R 3.6.3做出來的圖。很多粉絲可能用的都是最新版本的R 4.1.2。

我們知道R的版本在不停的更新，相應(yīng)的R包也在不停的更新。我把繪制氣泡圖和柱形圖相關(guān)的函數(shù)拿出來認(rèn)真的研究了一下，終于發(fā)現(xiàn)的癥結(jié)所在。

dotplot這個(gè)函數(shù)，多了個(gè) label_format 參數(shù)

我們來看看這個(gè)參數(shù)究竟是干什么用的，看看參數(shù)說明

label_format :

a numeric value sets wrap length, alternatively a custom function to format axis labels. by default wraps names longer that 30 characters

原來這個(gè)參數(shù)默認(rèn)值是30，當(dāng)標(biāo)簽的長(zhǎng)度大于30個(gè)字符就會(huì)被折疊，用多行來展示。既然問題找到了，我們就來調(diào)節(jié)一下這個(gè)參數(shù)，把他設(shè)置成100，讓我們的標(biāo)簽可以一行展示。

是不是還是原來的配方，還是熟悉的味道

同樣的柱形圖，我們也能讓他恢復(fù)原來的容貌。

關(guān)于如何使用R做GO和KEGG富集分析，可參考下文

GO和KEGG富集分析視頻講解