prochlo(seqinr)
prochlo()所属R语言包：seqinr
Zscore on three strains of Prochlorococcus marinus
Zscore 3株原绿球藻马里努斯
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This dataset contains the zscores computed with the codon model on all CDS from 3 strains of Procholorococcus marinus (as retrieved from Genome Reviews database on June 16, 2005)
这数据集包含zscores，3株的Procholorococcus马里努斯（2005年6月16日从基因组评价数据库检索与所有CDS的密码子模型计算）
用法----------Usage----------
data(prochlo)
格式----------Format----------
List of three dataframes of the zscore of each of the 16 dinucleotides on each CDS retrieved from the specific strain.
原价检索三个dataframes每个16二核苷酸在每个CDS zscore的从特定菌株。
BX548174 strain adapted to living at a depth of 5 meters (high levels of UV exposure)
AE017126 strain adapted to living at a depth of 120
AE017126应变适于居住在深度120
BX548175 strain adapted to living at a depth of 135
BX548175应变适于住在135的深度
参考文献----------References----------
are not depleted in light-exposed Prokaryotic genomes. Molecular Biology and Evolution, 23:2214-2219.<br> http://mbe.oxfordjournals.org/cgi/reprint/23/11/2214<br><br>
参见----------See Also----------
zscore
zscore
实例----------Examples----------
#[]
# Show the four YpY for the three ecotypes:[显示四个YPY三个生态型：]
#[]
data(prochlo)
oneplot <- function(x){
plot(density(prochlo$BX548174[, x]),
ylim = c(0,0.4), xlim = c(-4,4), lty=3,
main = paste(substr(x,1,1), "p", substr(x,2,2), " bias", sep = ""),
xlab="",ylab="",las=1, type = "n")
rect(-10,-1,-1.96,10, col = "yellow", border = "yellow")
rect(1.96,-1,10,10, col = "yellow", border = "yellow")
lines(density(prochlo$BX548174[, x]),lty=3)
lines(density(prochlo$AE017126[, x]),lty=2)
lines(density(prochlo$BX548175[, x]),lty=1)
abline(v=c(-1.96,1.96),lty=5)
box()
}
par(mfrow=c(2,2),mar=c(2,3,2,0.5) + 0.1)
oneplot("CT")
oneplot("TC")
oneplot("CC")
oneplot("TT")
#[]
# Show YpY biases with respect to light exposure[YPY显示光照射的偏见]
#[]
curdev <- getOption("device")
OK <- FALSE
devlist <- c("X11", "windows", "quartz") # interactive with width and height in inches[以英寸为单位的宽度和高度互动]
for(i in devlist){
if(exists(i) && identical(get(i), curdev)){
OK <- TRUE
break
}
}
if(OK){
curdev(width = 18, height = 11)
par(oma = c(0, 0, 3, 0), mfrow = c(1, 2), mar = c(5, 4, 0, 0), cex = 1.5)
example(waterabs, ask = FALSE) #left figure[左图]
par(mar = c(5, 0, 0, 2))
plot(seq(-5, 3, by = 1), seq(0, 150, length = 9), col = "white",
ann = FALSE, axes = FALSE, xaxs = "i", yaxs = "i")
axis(1, at = c(-1.96, 0, 1.96), labels = c(-1.96, 0, 1.96))
lines(rep(-1.96, 2),c(0, 150),lty=2)
lines(rep(1.96, 2), c(0, 150),lty=2)
title(xlab = "zscore distribution", cex = 1.5, adj = 0.65)
selcol <- c(6, 8, 14, 16)
z5 <- prochlo$BX548174[, selcol]
z120 <- prochlo$AE017126[, selcol]
z135 <- prochlo$BX548175[, selcol]
todo <- function(who, xx, col = "black", bottom, loupe){
dst <- density(who[, xx])
sel <- which(dst$x >= -3)
lines(dst$x[sel], dst$y[sel]*loupe + (bottom), col = col)
}
todo2 <- function(who, bottom, loupe){
todo(who, "CC", "blue", bottom, loupe)
todo(who, "CT", "red", bottom, loupe)
todo(who, "TC", "green", bottom, loupe)
todo(who, "TT", "black", bottom, loupe)
}
todo3 <- function(bottom, who, leg, loupe = 90){
lines(c(-5,-3), c(150 - leg, bottom + 20))
rect(-3,bottom,3,bottom+40)
text(-2.6,bottom+38, paste(leg, "m"))
todo2(who, bottom, loupe)
}
todo3(bottom = 110, who = z5, leg = 5)
todo3(bottom = 50, who = z120, leg = 120)
todo3(bottom = 5, who = z135, leg = 135)
legend(-4.5,110,c('CpC','CpT','TpC','TpT'),lty=1,pt.cex=cex,
col=c('blue','red','green','black'))
mtext(expression(paste("Dinucleotide composition for three ",
italic("Prochlorococcus marinus")," ecotypes")), outer = TRUE, cex = 2, line = 1)
}
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-9-30 01:22:37
