找到约 15 条结果

文章 rainbow函数取色

...行设置: With rainbow, the parameters start and end can be used to specify particular subranges of hues. The following values can be used when generating such a subrange: red = 0, yellow = 1/6, green = 2/6, cyan = 3/6, blue = 4/6 and magenta = 5/6. 譬如取色由红色到蓝色: ...

文章 R 语言colors()657种颜色

...个颜色名称具体对应的颜色,可以通过绘图呈现出来 pdf(file = "RColors.pdf",height = 20,width = 30)par(mar=c(0,0,0,0))plot(0, 0, type = "n", xlim = c(0, 1), ylim = c(0, 1), axes = FALSE, xlab = "", ylab = "")line=30col=22rect(  rep((0:(col - 1)/col)...

文章 R语言统计数据范围并用ggplot2绘制饼图

...ggplot2绘图饼图代码如下: library(reshape2) local({r <- getOption("repos") ;r["CRAN"] <- "http://mirrors.tuna.tsinghua.edu.cn/CRAN/" ;options(repos=r)}) library(ggplot2) library(cowplot) library(RColorBrewer) pairjoinC <- function(x,y){   ran1=paste(paste(head(x,-1),"%"...

文章 SNP指纹图谱软件SNPT

.../cgi-bin/snpt 这个软件可以做的分析: Indentify unique SNPs profiles and assign sequence types(MST);Calculate allele frequencies;Find informative SNPs;Calculate D (Index of the Discrininatory Ability);Find the set(s) of minimum SNPs;Output MST data file in mega and interleaved mega forma...

文章 快速生成iTOL配置文件美化你的进化树

...hylo_tree")tree_1 <- "abunt-tree.nwk"hub_1 <- create_hub(tree_1)data_file_1<- "abunt-metadata.txt"data_1 <- data.table::fread(data_file_1)# relabel by genusunit_1 <- create_unit(data = data_1 %>% select(ID, Genus),                      key = "itol_3al_1_labels",      ...

问题 变异注释

...的时候报错:Error: invalid record found in exonic_variant_function file (exonic format error): <line79synonymous SNVLOC119691921:XM_048633226.1#NC_063982.1#16995:exon3:c.C99T:p.L33L,LOC119691921:XM_048633233.1#NC_063982.1#16995:exon3:c.C99T:p.L33LNC_063982.11813318133CT0.43752219.779NC_0639...

文章 重测序群体遗传进化分析之—进化树构建

...\pop:/work omicsclass/pop-evol-gwas:v1.3#对vcf文件进行数据过滤vcftools --gzvcf all.varFilter.vcf.gz --recode --recode-INFO-all --stdout     --maf 0.05  --max-missing 0.7  --minDP 4  --maxDP 1000      \    --minQ 30 --minGQ 0 --min-alleles 2  --max-allel...

文章 安装R包的几种方法

...,repos = NULL,type = "source") 3.R包下载到本地后安装 download.file("https://cran.r-project.org/src/contrib/Archive/rvcheck/rvcheck_0.1.8.tar.gz","rvcheck_0.1.8.tar.gz") install.packages("rvcheck_0.1.8.tar.gz",repos = NULL) 4.命令行安装 在shell的终端sudo R CMD INSTALL packag...

文章 SNP 过滤标准保证数据质量及参考文献:

...: https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering SNP gatk VariantFiltration \ -V snps.vcf.gz \ -filter "QD < 2.0" --filter-name "QD2" \ -filter "QUAL < 30.0" --filter-name "QUAL30" \ -filter "SOR...

问题 R语言分析GEO数据,您好老师,19年参加培训的时候就是用的R3.6.1,自己运行出现如下报错

...HuRSTA-2a520709 Library - package hursta2a520709cdf not installed Bioconductor - hursta2a520709cdf not available > options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor") > > if(!requireNamespace("BiocManager", quietly = TRUE)){ + install.packages("BiocManager") + }>...

问题 perl双层哈希赋值

...qIO;use Bio::Seq;use Data::Dumper;#输入序列$in = Bio::SeqIO->new( -file   => "C:/Users/Administrator/cds.fa", -format => 'Fasta'); #读取IDmy $count=-1;my %ID;open IN, "C:/Users/Administrator/KAKS.txt" or die "$!";        #这个文件是blast输出并经过筛选的结果。 ...

文章 STAMP使用(组间差异)

...2)样本信息表 2.步骤     (1)打开软件:点击左上角 file --> load data     (2)输入文件1,2     (3)点击OK得到如下结果,粉色标记下选择图片类型,黄色标记下可更改图片大小,标注等     (4)在左侧选择要比较的分...

文章 利用SNP构建指纹图谱!SNPT的使用教程!

...ec/cgi-bin/snpt这个软件可以做的分析: Indentify unique SNPs profiles and assign sequence types(MST);Calculate allele frequencies;Find informative SNPs;Calculate D (Index of the Discrininatory Ability);Find the set(s) of minimum SNPs;Output MST data file in mega and interleaved mega forma...

问题 KNN补值函数knnImputation函数的距离计算问题

... if (length(tgt.nas) == 0) warning("No case has missing values. Stopping as there is nothing to do.") xcomplete <- dm[setdiff(distInit:N, nas), ] if (nrow(xcomplete) < k) stop("Not sufficient complete cases for computing neighbors.") for (i in tgt.nas) { ...

文章 Mfuzz做时间聚类分析

...量 gene <- read.table("gene_fpkm.txt",header =T,row.names=1,sep="\t", check.names = F) head(gene) 基因表达量数据格式如下: ID 0h 1h 2h 3h 4h ENSGALG00000000003 0.0000000 0.01421203 0.08885999 0.01337165 0.0000000 ENSGALG00000000011 11.3414235 8.40606978 9.13251124 8.91866821 9.575...