similar to: ggplot zoomin

I have two data matrices that I want to make the correlation between each column from data1 and each column from data 2 and also calculate the p-value Matrices dont have the same size and I tried such a script. > bg <- read.table (file.choose(), header=T, row.names) > bg > Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172

I am trying to find the percentage of the parameters explaining the bacterial community composition. I have one data matrix with relative abundance of OTUs and one with environmental parameters. I used varpart in vegan package but the values in the venn diagram is bigger than 100% in total.How is it possible? What might be the reason? Thank you library(vegan) gotud <-

Hello, I have a very data matrix and I have a file which has the names that I need to subset. However I cannot manage to subset the main file. ANy idea? bg <- read.table (file.choose(), header=T, row.names) bg Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218 Gi20Jun11 0.001217

Dear All, When I plot the values and linear regression line for one data set, it is fine. But for another one I see zigzags, when I plot the confidence interval >cd Depth CHAOsep12RNA 9,94 804 25,06 1476,833333 40,04 1540,561404 50,11 1575,166667 52,46 349,222222 54,92 1941,5 57,29 1053,507042 60,11 1535,1 70,04 2244,963303 79,97 1954,507042 100,31 2679,140625 >

Hello, I calculate the correlation between two matrices cor(x,y, method="spearman") and I am wondering if it possible to see only the significant correlations. I can do that for single OTUs with cor.test() command but I would like to have an output for whole matrix. Besides,I would like to plot the relative abundance of each OTU, against the number of significant pair-wise correlations

Dear All, I am trying to perform MANOVA. I have table with 504 columns(species) and 36 rows) with two grouping (season and location) Zx <- Z[c(4:504)] Zxm <- as.matrix(Z) m<- manova(Zxm~Season*location, data=Z) when I do summary.aov, I get respond for each species but summary.manova summary.manova(m) :" residuals have rank" 24<501. What can it be the reason for this error

Hello - I am trying to plot flows in a number of rivers within the same plot, and need to colour the lines differently, using a colour-blind palette. Code beneath works but has colours assigned by the program I have made some simple dummy data: ## code 1 cb8<- c("#000000", "#E69F00", "#56B4E9", "#009E73","#F0E442", "#0072B2",

Hello all, I've been using the following qplot command: qplot(pixX,pixY, data=som, geom="tile", fill=rgb) + scale_fill_identity() + opts(aspect.ratio = .75) + facet_grid(unitX ~ unitY) Now I would like to convert it into the explicit ggplot grammar, so I can remove the extras: axes, labels, background, borders, facet labels, and extra white-space around the plot. (If anyone has

Hi, When I zoom into a graph created in ggplot2 with the coord_cartesian(ylim=c(0,5)) option, I have no values labelled on my y-axis. For this graph ggplot2 only puts labels the y-axis at intervals of 10 (i.e. 0, 10, 20, ...). However, the major portion of the graph I am interested in is located between the values of 0 and 5 on the y-axis (thus why I am zoooming). How can I coerce ggplot2 into

Dear R users, I am working on a data-set with 3 species. They are apple, orange and banana. I want to annotate the facets only on the bottom panel. However, by default I am getting annotations on all the plots. I was able to get text annotation only on the desired plot. However, I am confused what I need to do for the arrows / segments. Here is my code: library(ggplot2) library(grid) tempobs

This patch makes windows zoom in and out of a zero point on create/unmap. I've cleaned up the formatting/style to be consistent with the rest of compiz (eg adding spaces around operators, tabifying, using C style comments). This patch could use some more work. It should only apply to decorated toplevels, but right now it also affects XUL menus (I guess because they are not unmanaged like

Hi, I am running the following code: mfg0 <- ggplot(aes(x=Grade,y=Math,colour=RiskStatic45678),data=math.f) mfg1 <- mfg0 + geom_smooth(method="lm", formula=y ~ ns(x,2),size=1) + geom_smooth(aes(y=nalt.math,color="NALT"),size=1,data=nalt) + scale_colour_brewer("Risk Status", pal="Set1") + coord_cartesian(ylim = c(175, 245)) mfg1 And when I specify

Dear Colleagues, In the following simple ggplot2 code: -------------------------------- m <- ggplot(d.fig, aes(time, prob)) m + stat_summary(fun.data = "median_hilow", conf.int = .95, geom = "smooth") + facet_wrap(~ Cohort, nrow=1) + coord_cartesian(ylim = c(0, .03)) -------------------------------- Is there a way to replace the y-axis label from "prob" to

Hello everyone, I am using ggplot to plot but I am getting the following error which I do not understand Error: geom_text requires the following missing aesthetics: label My code is dimx<-256 library(ggplot2) dev.new() xandy<-expand.grid(seq(1:dimx),seq(1:dimy)) xx<-data.frame(xandy[[1]],xandy[[2]],Powermap=Powermap) subsetxx<-subset(xx, xx$Powermap>threshold)

Background: OS: Linux Mandrake 10.1 release: R 2.0.0 editor: GNU Emacs 21.3.2 front-end: ESS 5.2.3 --------------------------------- Colleagues Is there a function in R that is an equivalent of zoom in matlab? This is very useful for being able to magnify details in a plot. I have searched the help for "zoom", "interactive zooming", and "magnify". The R search

hello, how can I do to drop C from this character "C325" ? _____________________________________________________________________________ [[alternative HTML version deleted]]

Full_Name: Jerome Asselin Version: 1.3.0 OS: Windows 98 Submission from: (NULL) (24.77.112.193) I have a hard time to magnify the axis annotations in barplot() Here are some examples: #This one has no effect. barplot(1:3,names.arg=1:3,cex.axis=3,xlab="x",ylab="y") #This one magnifies the x and y labels

Hello, I got stuck with a graphics question: I've 3 figures that I present on a single page (window) via 'layout'. The layout is layout(matrix(c(1,1,2,3), 2, 2, byrow=TRUE)); so that the frst plot spans the both columns in row one. Now I'd like to magnify the fist figure so that it takes 20% more vertical space (i.e. more space for the y-axis). How would I do this in R?

I've been trough the R documentation for about half an hour and it's not clear to me how to do this: I need to format to character a series of integers from 1 to 1000, and I like them to look like "0001" "0002", "0059", "0123" and so on. Padded with zeroes to have four digits. Cheers! Mario. r-help-request at r-project.org wrote: > Send

Hello, i use ggplot to plot some measures including CIs as horizontal errorbars. I get an error when the scale limits are narrower than the boundaries of the error bar and hence the CIs are not plotted. library(ggplot2) df <- data.frame(resp=c(1,2), k=c(1,2), se=c(1,2)) ggplot(df, aes(resp,y=k)) + geom_point() + geom_errorbarh(aes(xmax = resp + se, xmin = resp - se)) +