Using prcomp/princomp for PCA in R (二)

############################### PCA ############################### install.packages(“vegan”) library(vegan) > STpcoa<-read.table(file=”bactera_16s_final.subsample.phylip.tre1.weighted.phylip.pcoa.axes”, header=T,row.names=1) > STpcoa axis1 axis2 axis3 axis4 Cellulose -0.020878[……]

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Using prcomp/princomp for PCA in R (一)

Difference between prcomp and princomp: ‘princomp’ can only be used with more units than variables” prcomp是基于SVD分解(svd()函数,princomp是基于特征向量eigen()函数) Good video source: http://www.youtube.com/watch?v=oZ2nfIPdvjY http://www.youtube.com/watch?v=I5GxNzKLIoU&feature=relmfu http://ww[……]

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4sample CA RDA analysis

  > gtsdata_test=read.table(“gtsdata.txt”, header=T) > gtsenv=read.table(“gtsenv.txt”, header=T) > gtsdata_data_t<-t(gtsdata_data) > decorana(gtsdata_data_t) Call: decorana(veg = gtsdata_data_t) Detrended correspondence analysis with 26 segments. Rescaling of axes w[……]

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基于Vegan 软件包的生态学数据排序分析学习

“基于Vegan 软件包的生态学数据排序分析 赖江山 米湘成 (中国科学院植物研究所植被与环境变化国家重点实验室,北京 100093) 摘要:群落学数据一般是多维数据,例如物种属性或环境因子的属性。多元统计分析是群落生态学常用的分析方法,排序(ordination)是多元统计最常用的方法之一。CANOCO是广泛使用的排序软件,但缺点是商业软件价格不菲,版本更新速度也很慢。近年来,R语言以其灵活、开放、易于掌握、免费等诸多优点,在生态学和生物多样性研究领域迅速赢得广大研究人员的青睐。R语言中的外在软件包“Vegan”是专门用于群落生态学分析的工具。Vegan能够提供所有基本的排序方法,同时[……]

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R OTU heatmap2

source(“http://www.bioconductor.org/biocLite.R”); biocLite(“affy”); biocLite(“Biobase”); library(affy); library(Biobase); >bac_4sampledata=read.csv(“/home/R_heatmap/4sample_R_cluster.csv”, sep=”\t”) > row.names(bac_4sampledata)<-bac_4sampledata$Group > bac_4sample_Datamatrix<[……]

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454 pyrosequencing analysis pipeline

mothur > sffinfo(sff=454Reads_archaea.sff, flow=T) Extracting info from 454Reads_archaea.sff … 10000 20000 30000 40000 50000 60000 70000 80000 90000 92115 It took 68 secs to extract 92115. Output File Names: 454Reads_archaea.fasta 454Reads_archaea.qual 454Reads_archaea.flow m[……]

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My PROJECT

Amoa project A2,A3 amoa sample sequencing (1) use geneious to deal with the sequence raw data, get 635bp DNA sequence (2)use mafft to get the alignment results (3)mothur deal pipline mothur > dist.seqs(fasta=AMOA_A2A3.mafft.align.shortname.fasta, output=lt) 0 0 59 0 Output[……]

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