similar to: Newbie question about the use of lm and anova

Hello, Apologies if this is the wrong list, I am a first-time poster here. I have an experiment in which an output is measured in response to 42 different categories. I am only interested which of the categories is significantly different from a reference category. Here is the summary of the results: summary(simple.fit) Call: lm(formula = as.numeric(as.vector(TNFa)) ~ Mutant.ID, data =

Hello all, Sorry if this is an FAQ. I have been trying to search the archives without success. I have a dataset (ChiPs microarray) where the experiment to experiment variability is very high but where within an experiment, the data nearly always goes in the "right" (hypothesis confirming) direction. I am trying to figure out the right way to use R to do the statistics and generate

Hello all, Sorry if this is an FAQ. I have been trying to search the archives without success. I have a dataset (ChiPs microarray) where the experiment to experiment variability is very high but where within an experiment, the data nearly always goes in the "right" (hypothesis confirming) direction. I am trying to figure out the right way to use R to do the statistical analysis and

Hi list, In the following code, how can I place the percentage label away from numbers in the second y-axis (lets say all should be inside plot area)? Thanks Alireza ================= require(grid) vp<- viewport(x=.1,y=.1,width=.6,height=.6,just=c("left", "bottom")) pushViewport(vp)

Hi, I am learning xyplot. I have an example dataset attached. plotdata<-read.table("plotdata.txt",sep='\t',header=T,row.names=1) head(plotdata,n=4) y x type 1 -4.309601 -0.7448405 A 2 -4.715421 0.7875994 A 3 -2.310638 0.5455310 A 4 -2.685803 10.4116868 A xyplot(y~x,groups=type,plotdata, auto.key=T) This shows different colors for different

Hi list, Does any body know how I can create a margin area around the graphic created by xyplot (the same thing we do using par in plot function)? I tried viewport, but does not work. Here is the code: ============================================== require(grid) vp<- viewport(x=.1,y=.1,width=.6,height=.6,just=c("left", "bottom")) pushViewport(vp)

Hello, everybody. We are working on a tool for mutation testing. The work is still in progress and far away from being done. However, we have got some results already. And we would like to share them with you. But, let me give you a brief introduction first. ### Mutation Testing In a nutshell, Mutation Testing is a way to evaluate a quality of a test suite. The approach suggests introducing a

This is really a question of how to program this *BETTER*. It works as I have done it, but is quite ugly. I want to do a 3d scatterplot of the upper triangle of a matrix, where the z-values are the values in the matrix, and the row and column indices are the y- and x-values. The complete (11 by 11) matrix is mmtop94.2. Here is my awkward code: mmtop94.2[lower.tri(mmtop94.2)] <- NA # Here i

Hello everyone. I am using ggplot and I need some help to merge these two plots into one. plot_CR<-function(x,y,agentid,CRagent){   library(ggplot2)     agent<-CRagent[[agentid]] # To make following expression shorter   ggplot((data.frame(x=CRX,y=CRY,sr=agent$sr)))+   geom_point(aes(x,y,colour=cut(sr,c(0,-10,-20,-30,-40,-50,-60,-70,-80))))+   geom_text(aes(x,y,color=cut(sr,

Dear all, today I have writted the following code, to plot the contents of some matrices I have plot_shad_f function(f){ library(ggplot2) dev.new() plotdata<-melt(f) names(plotdata)<-c('x','y','z') v<-ggplot(plotdata, aes(x, y, z = z)) print(v + geom_tile(aes(fill=z))) } I would like to ask your help add a small circle in this plotting. What would be

Hi all, I've been trying (unsuccessfully) to modify an xyplot I created using the lattice package. I would like to change default strip colors and locations. I started with numeric data in 4 columns, which look like this: 0.25 2 1 32 0.25 2 2 30 0.25 2 3 27 0.25 2 4 23 0.25 2 5 17 0.25 3 1 30 0.25

Dear All, I am trying to build a simple ggplot, but where the scale is reversed, i.e. the largest numbers are on the bottom. An example of the code I am using is > plotdata<-data.frame(x=1:10, y=runif(10)) > plot<-ggplot() > plot<-plot+layer(data=plotdata, mapping=aes_string(x='x',y='y'), geom='point', stat='identity', size=4) >

Hello All, This will probably be easy for some but isn't for me. Currently am working on a text mining exercise. Want to be able to predict whether cancer patients got KRAS testing, and, if so, whether the test yielded a result of wild type/negative or mutant/positive. I've begun with a "bag-of-words approach" that looks at the count of specific terms in the medical records and

Hello R help mailing list, I'm having difficulty saving a series of figures in an analysis. I have attempted to save them in a for loop with the following code: for(i in 1:20){ sF<-paste("fig",i,".jpeg",sep="") jpeg(file=sF,width=600,height=500,quality=100,pointsize=12) attach(plotData) xyplot(CHC~1:13), detach(plotData) graphics.off() } If I break

I am trying to plot some data, but have got some difficulties with labels on the tick marks on the x-axes. There are 20 data points. All I want to do is to plot the Loss versus Lines. When I use xyplot, the first tick mark starts from 2 rather than 1, and also there is a NA as the final tick mark. Here is the R code you code give it a try: Would any body be able to fix this, please?

Hello All, Started out awhile ago trying to select columns in a dataframe whose names contain some variation of the word "mutant" using code like: names(KRASyn)[grep("muta", names(KRASyn))] The idea then would be to add together the various columns using code like: KRASyn$Mutant_comb <- rowSums(KRASyn[grep("muta", names(KRASyn))]) What I discovered though, is

Hey Paul, Thanks for the reply! If you wanted you could try my radio stream, http://stream.socorock.com:8000/socorock.ogg.m3u - that's really good news, I think I'm gonna pick up one of these things soon! What a great way to listen to radio. Cheers, Jordan On 02/26/2012 12:01 AM, Paul Webster wrote: > The Grace and Logitech devices can play streaming OGG. I have different models of

Is there a canonical means to apply a function over multiple arrays simultaneously? For example, if I wanted to plot each line with a different color? Or is a for loop conversion my best option? x <- seq(0, 8, by = 2) y <- matrix(1:15, nrow = 5, byrow = TRUE) my.colors <- heat.colors(3) drawLines <- function(row) { lines(x, row) # want corresponding 'my.colors' here }

Dear UserRs, I am trying to use systematically ggplot2 for most of my plots, but I am fighting some lack of documentation, which I try to overcome. I want to build a scatterplot where the axes cross exactly at (0,0). I tried using scale_y_continuous(limits=c(0,10)), but I always get an extra space at the bottom of the axes. The code I used is below. > plotdata<-data.frame(x=1:10,

Dear All (probably Hadley), I am now trying to customise some plots using a bar geom. I do not want to use the default binning statistic, but rather calculate the bar heigths separately. I do manage this, but for comparison purposes I would like to have a set of plots all with the same y-axis height. But I do not seem to find out how to fix the scale of the y-axis in this case. Any tips?