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ggplot2绘制Pathway富集分析气泡图

[에어 프라이어] 스콘 만들기 재생수205 | 등록2018.11.14. 신고
좋아요 댓글 0 나중에 보기

>library(ggplot2) #载入ggplot2

>pathway=read.table(“KEGG.enrichment.txt”,,header=T,sep=”\t”)
#读取数据

>pathway=head(read.table(“KEGG.enrichment.result.txt”,header=T,sep=”\t”),n=20)
#读取数据前20行

> p = ggplot(pathway,aes(enrichFactor,Term_Name))
#以富集因子和pathway名称为X轴和Y轴

  • geom_point(aes(size=GeneHitsInSelectedSet,color=-1*log10(Qvalue)))
    #点图大小和颜色数据
    +scale_colour_gradient(low=”green”,high=”red”) #颜色变化
    +labs(color=expression(-log10),size=”Gene
    number”,x=”Rich factor”,y=”Pathway name”,title=”Top20 of pathway
    enrichment”) #标签名称

> pr=pr+theme_bw()

> pr

(1)火疗方1

“나중에 보기”에 저장되었습니다.

皇家国际官网 1

组方
防风20g、麻黄10g、桂枝10g、细辛6g、秦艽20g、威灵仙20g、附子20g、肉桂20g、川芎20g、当归20g、生姜20g、艾叶30g、伸筋草30g、透骨草30g、丝瓜络20g、鸦胆子30g。

퍼가기 펼침

KEGG.enrichment.result.jpg

功效 祛风通络,散寒除湿。

▶재료 (플레인 4개, 초코칩 4개 분량, 약 1시간 30분소요)박력분 225g,
베이킹파우더 7g, 설탕 27g, 소금 2g, 버터 27g, 우유 130g, 초코칩 40g1)
볼에 박력분, 베이킹파우더, 소금을 넣고 섞어줍니다2) 버터를 넣고 손으로
눌러 콩알만 해지도록 가루와 섞어가며 쪼개줍니다3) 버터가 작아지면 설탕을
넣고 섞은 다음 우유를 부어 뭉쳐줍니다4) 많이 끈적거리면 덧 가루를 뿌려
반으로 갈라 한군데에 초코 칩을 넣고 뭉쳐줍니다5) 반죽은 랩으로 감싸
냉장실에 30분~1시간 가량 둡니다6) 에어 프라이어를 160도 10분간 아무것도
넣지 않고 돌려줍니다+ 이때 종이호일을 넣지 않습니다 (가벼운 종이가 에어
프라이어 안에 날려 열선과 닿을 수 있습니다) = 경험담7) 예열 하는 동안
반죽 하나를 꺼내 4등분 잘라줍니다8) 종이호일을 에어 프라이어에 대충 깔아
반죽을 올립니다 + 이때 계란 물을 바르면 더 먹음직스럽게 구워집니다9)
에어 프라이어를 160도 15분간 돌립니다10) 반죽을 뒤집어 5분간 더
돌립니다11) 남은 반죽도 같은 방법으로 굽습니다12) 잼을 발라 먹거나 그냥
먹어도 됩니다

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_皇家国际官网,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

主治 肢体关节肌肉酸痛,游走不定。

这是参考以下教程用自己的数据实现一遍,

(2)火疗方2

R语言ggplot2画图系列——Pathway富集分析气泡图 – 生信技能树 – Powered by
Discuz!
http://www.biotrainee.com/forum.php?mod=viewthread&action=printable&tid=927

组方
川乌30g、草乌30g、麻黄10g、桂枝10g、白芍20g、川芎20g、当归20g、羌活20g、独活20g、防风20g、秦艽20g、威灵仙20g、附子30g、细辛6g、艾叶30g、伸筋草30g、透骨草30g、丝瓜络20g、鸦胆子30g。

R语言ggplot2绘图教程——Pathway富集分析气泡图 – CSDN博客
http://blog.csdn.net/sinat\_38163598/article/details/72827851

功效 温经散寒,祛风除湿。

主治 肢体关节肌肉疼痛较剧,痛有定处,得热痛减,遇寒痛增,局部不红不热。

(3)火疗方3

组方
薏苡仁30g、苍术20g、白术20g、茯苓20g、羌活20g、独活20g、防风20g、川乌30g、草乌30g、麻黄20g、桂枝20g、当归20g、川芎20g、生姜20g、秦艽20g、艾叶30g、伸筋草30g、透骨草30g、丝瓜络20g、鸦胆子30g。

功效 除湿通络,祛风散寒。