Dear BioCs, I'd like to receive some help of you. I need to plot a growth curve (which I already did) with standard deviation bars (which I didn't do yet). I already have the standard deviation values calculated. I believe I can read the file containing those values and plot above the points in my graphic, or calculate those values using R, and plot then. Can you help me giving some suggestions? tabela=read.table("irradiacao2.txt",sep="\t",skip=1) tabelan2=tabela[,2:7] colnames(tabelan2)=c("Pre-irradiation","0H","4H","24H","48H","96H") rownames(tabelan2)=tabela[,1] tabela2 = as.matrix(tabelan2) plot(tabela2[1,],type="l", col=" blue", bty="o", lty=1, font.main=2, ylim=c(10000000,120000000), main="Growth curves", ylab="cell number", xlab="Hours after treatment", xaxt="n") points(tabela2[1,], pch=1, col="blue", cex=1.0) axis(1, at=1:6, labels=colnames(tabelan2)) lines(tabela2[2,],type="l", col="black") points(tabela2[2,], pch=1, col="black", cex=1.0) lines(tabela2[3,], type="l",col="blue") points(tabela2[3,], pch=2, col="blue", cex=1.0) lines(tabela2[4,],type="l", col="black") points(tabela2[4,], pch=2, col="black", cex=1.0) legend("topleft", cex=0.9, legend=c("Control RI", "Treated RI", "Control RII", "Treated RII"), lty=c(1,1,1,1), pch=c(1,2,1,2), col=c("blue", "blue", "black", "black")) -- Priscila Grynberg, B.Sc., M.Sc. Doutoranda em Bioinformática (Bioinformatics D.Sc student) Laboratório de Genética Bioquímica Universidade Federal de Minas Gerais Tel: +55 31 3409-2628 CV: http://lattes.cnpq.br/8808643075395963 [[alternative HTML version deleted]]

Dear Priscila, if you have already computed the values you can easily plot the bars using the arrows() function. Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland Priscila Grynberg <priscilag at="" gmail.="" com=""> To Sent by: bioconductor at stat.math.ethz.ch bioconductor-boun cc ces at stat.math.eth z.ch Subject [BioC] Standard deviation 24.08.2009 14:08 Dear BioCs, I'd like to receive some help of you. I need to plot a growth curve (which I already did) with standard deviation bars (which I didn't do yet). I already have the standard deviation values calculated. I believe I can read the file containing those values and plot above the points in my graphic, or calculate those values using R, and plot then. Can you help me giving some suggestions? tabela=read.table("irradiacao2.txt",sep="\t",skip=1) tabelan2=tabela[,2:7] colnames(tabelan2)=c("Pre-irradiation","0H","4H","24H","48H","96H") rownames(tabelan2)=tabela[,1] tabela2 = as.matrix(tabelan2) plot(tabela2[1,],type="l", col=" blue", bty="o", lty=1, font.main=2, ylim=c(10000000,120000000), main="Growth curves", ylab="cell number", xlab="Hours after treatment", xaxt="n") points(tabela2[1,], pch=1, col="blue", cex=1.0) axis(1, at=1:6, labels=colnames(tabelan2)) lines(tabela2[2,],type="l", col="black") points(tabela2[2,], pch=1, col="black", cex=1.0) lines(tabela2[3,], type="l",col="blue") points(tabela2[3,], pch=2, col="blue", cex=1.0) lines(tabela2[4,],type="l", col="black") points(tabela2[4,], pch=2, col="black", cex=1.0) legend("topleft", cex=0.9, legend=c("Control RI", "Treated RI", "Control RII", "Treated RII"), lty=c(1,1,1,1), pch=c(1,2,1,2), col=c("blue", "blue", "black", "black")) -- Priscila Grynberg, B.Sc., M.Sc. Doutoranda em Bioinform?tica (Bioinformatics D.Sc student) Laborat?rio de Gen?tica Bioqu?mica Universidade Federal de Minas Gerais Tel: +55 31 3409-2628 CV: http://lattes.cnpq.br/8808643075395963 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com

Hello, try having a look at the plotCI function from gplots, for plotting error bars and confidence intervals. Cheers \Heidi > Dear BioCs, > I'd like to receive some help of you. I need to plot a growth curve (which > I > already did) with standard deviation bars (which I didn't do yet). > > I already have the standard deviation values calculated. I believe I can > read the file containing those values and plot above the points in my > graphic, or calculate those values using R, and plot then. > > Can you help me giving some suggestions? > > tabela=read.table("irradiacao2.txt",sep="\t",skip=1) > tabelan2=tabela[,2:7] > colnames(tabelan2)=c("Pre-irradiation","0H","4H","24H","48H","96H") > rownames(tabelan2)=tabela[,1] > tabela2 = as.matrix(tabelan2) > > plot(tabela2[1,],type="l", col=" blue", bty="o", lty=1, font.main=2, > ylim=c(10000000,120000000), main="Growth curves", ylab="cell number", > xlab="Hours after treatment", xaxt="n") > points(tabela2[1,], pch=1, col="blue", cex=1.0) > axis(1, at=1:6, labels=colnames(tabelan2)) > lines(tabela2[2,],type="l", col="black") > points(tabela2[2,], pch=1, col="black", cex=1.0) > lines(tabela2[3,], type="l",col="blue") > points(tabela2[3,], pch=2, col="blue", cex=1.0) > lines(tabela2[4,],type="l", col="black") > points(tabela2[4,], pch=2, col="black", cex=1.0) > legend("topleft", cex=0.9, legend=c("Control RI", "Treated RI", "Control > RII", "Treated RII"), lty=c(1,1,1,1), pch=c(1,2,1,2), col=c("blue", > "blue", > "black", "black")) > > > -- > Priscila Grynberg, B.Sc., M.Sc. > Doutoranda em Bioinform?tica (Bioinformatics D.Sc student) > Laborat?rio de Gen?tica Bioqu?mica > Universidade Federal de Minas Gerais > Tel: +55 31 3409-2628 > CV: http://lattes.cnpq.br/8808643075395963 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor