[R] PCA and gglot2

Hi, I was trying as well as looking for an answer without success (a bit strange since it should be an easy problem) and therefore I will appreciate you help: My simple script is: # Loadings data of 5 columns and 100 rows of data data1<-read.csv("C:/…/MyPCA.csv") pairs(data1[,1:4]) pca1 <- princo

Re: [R] PCA and gglot2

Hi, Thanks. Fig 4 in the link you provided is what I am looking for. I still do not know how to implement my data1 and pca1 in the script you provided as I think it is only a part of a full script. " data1<-read.csv("C:/…/MyPCA.csv") pca1 <- princomp(data1[,1:4], score=TRUE, cor=TRUE) " Am I ri

Re: [R] PCA and gglot2

Dear John, Thanks for the help. I did some minor modifications to your script as I had some problems: ... pca = PCA(data[,1:4], scale.unit=T, graph=F) dat1 <- data.frame(pca$scores) # creates the data.frame dat1$items <- rownames(data$group) # adds item names ggplot(dat1, aes(pca$ind$coord[

Re: [R] PCA and gglot2

Hi, Thanks to ssefick for the ggbiplot tip. It works fine so I submit a general script thats works for future users. library(ggbiplot) data<-read.csv("C:/…/MyPCA.csv") data1<-data[,1:4] my.pca <- prcomp(data1, scale. = TRUE) my.class<- data$Group g <- ggbiplot(my.pca, obs.scale = 1, var.scal

[R] What is “Proportion of trace” in lda (MASS)

Hi, Is the lda function (R MASS package) “Proportion of trace” is similar to “proportion of variance explained”in the case of PCA? How can I store the LD1 and LD2 in two separate variables? Thanks -- View this message in context: http://r.789695.n4.nabble.com/What-is-Proportion-of-trace-

[R] GUI tools for R

Hi, I wish to build a GUI for my R script, what are the best and easiest tools to use and which ones as good documentation or books? Thanks -- View this message in context: http://r.789695.n4.nabble.com/GUI-tools-for-R-tp4673925.html Sent from the R help mailing list archive at Nabble.com.

[R] Image Gray Level Co-occurrence Matrix in R

Hi, I've been looking for Image Processing packages without success. I am mainly interested in image Gray Level Co-occurrence Matrix (GLCM) parameters like Contrast, Correlation, Energy, Homogeneity. Is there a package that can do it? Any ideas, comments, etc are welcome. Thanks. -- View

[R] Mark each group centroid in a linear discriminant analysis plot

Hi, How can I calculate and mark each group centroid in a linear discriminant analysis plot (using ggplot2)? Script: ## originate from http://r.789695.n4.nabble.com/LDA-and-confidence-ellipse-td4671308.html require(MASS) require(ggplot2) iris.lda<-lda(Species ~ Sepal.Length + Sepal.Width + Peta

[R] Scatterplot matrix - Pearson linear correlation and Density Ellipse

Hi, I have modified a known script to generate a scatterplot matrix: panel.cor = function(x, y, digits=2, prefix="Rho=", cex.cor) { usr = par("usr"); on.exit(par(usr)) par(usr = c(0, 1, 0, 1)) r = abs(cor(x, y, use="pairwise.complete.obs", method = "pearson")) txt = format(c(r,

Re: [R] Scatterplot matrix - Pearson linear correlation and Density Ellipse

Hi, I used the pairs.panels() in pkg:psych and it is helpful. It saves time. but if I use this line: pairs.panels(cfcap[8:11], scale = FALSE, lm=TRUE,ellipses=TRUE, digits = 2 ) The results are: - The upper.panel does not show the pearson r but the lm data. Furthermore, can I use the pairwise

Re: [R] Scatterplot matrix - Pearson linear correlation and Density Ellipse

Thanks a lot for the answer -- View this message in context: http://r.789695.n4.nabble.com/Scatterplot-matrix-Pearson-linear-correlation-and-Density-Ellipse-tp2763552p2953909.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-pr

Re: [R] Scatterplot matrix - Pearson linear correlation and Density Ellipse

Hi, strangely, when I run this script: panel.cor = function(x, y, digits=2, prefix="r=", cex.cor) { usr = par("usr"); on.exit(par(usr)) par(usr = c(0, 1, 0, 1)) r = abs(cor(x, y, use="pairwise.complete.obs", method = "pearson")) txt = format(c(r, 0.123456789), digits=digits)[1]

[R] Xlsx and R -read problem

r in .jnew("java/io/FileInputStream", file) : java.io.FileNotFoundException: Can someone tell me what is the problem? and how to solve it. Cheers, Ashz -- View this message in context: http://r.789695.n4.nabble.com/Xlsx-and-R-read-problem-tp2998304p2998304.html Sen

[R] Sine function fitting

Hi, Is there a package to perform a sine function fitting to XY data? Thx, Ashz -- View this message in context: http://r.789695.n4.nabble.com/Sine-function-fitting-tp3000156p3000156.html Sent from the R help mailing list archive at Nabble.com

[R] points(x,y), mean and standard deviation

Hi, I have a data set with 3 rows (X=date, Y1=arithmetic mean and Y2=standard deviation). How can I create a graph(e.g., points) which will show the +-stdev as well (similar to excel). Thanks -- View this message in context: http://r.789695.n4.nabble.com/points-x-y-mean-and-standard-deviatio

Re: [R] points(x,y), mean and standard deviation

Hi, Thanks for the tip. I run this script: means.cl <- c(82, 79, 110, 136,103) stderr.cl <- c(8.1,9.2,7.4,1.6,7.6) plotCI(x = means.cl , uiw = stderr.cl, pch=24) But how can I connect the mean triangles with a line? Thanks -- View this message in context: http://r.789695.n4.nabble.com/poin

[R] ggplot - unwanted sorted X values

Hi, I have this script: dat <- data.frame(X = halistat$Date,Y1 = halistat$avg,Y2 = halistat$stdev) ggplot(data = dat, aes(x = X, y = Y1, ymin = Y1 - Y2, ymax = Y1 + Y2)) + geom_point() + # points at the means geom_line() + # if you want lines between pints geom_errorbar() # error bars, Y1

[R] ggplot output

Dear All, I have this script: dat <- data.frame(Month = hstat$Date,C_avg = hstat$C.avg,C_stdev = hstat$C.stdev) ggplot(data = dat, aes(x = Month, y = C_avg, ymin = C_avg - C_stdev, ymax = C_avg + C_stdev)) + geom_point() + geom_line() + geom_errorbar() dat <- data.frame(Month = hstat$D

Re: [R] ggplot output

Dear Thierry, Your solution looks very elgant but I can not find a proper example. Can you provide me one? Thx -- View this message in context: http://r.789695.n4.nabble.com/ggplot-output-tp3027026p3027108.html Sent from the R help mailing list archive at Nabble.com. ___

[R] Matrix Plot and linear regression

Hi, Is it possible to do a Matrix Plot and in the cell perform a linear regression also adding to the cell the r2 and the equation. If so, how? Thanks, As hz -- View this message in context: http://r.789695.n4.nabble.com/Matrix-Plot-and-linear-regression-tp2321613p2321613.html Sent from the R

[R] Automated plot and linear regression line/data

Hi, I have an excel sheet (already imported to R) with multiple columns and I am looking for a way in R that will allow me to generate a plot for every possible pair and its linear regression line/data. Any tip/idea/script how do to so. Thanks, As hz -- View this message in context: http://

Re: [R] Automated plot and linear regression line/data

Hi, I presume the easy way is using plot and lm. Thx, As hz -- View this message in context: http://r.789695.n4.nabble.com/Automated-plot-and-linear-regression-line-data-tp2328027p2328372.html Sent from the R help mailing list archive at Nabble.com. ___

[R] Linear regression equation and coefficient matrix

Hi, I have 20*60 data matrix (with some NAs) and I wish to perfom a Pearson correlation coefficient matrix as well as simple linear regression equation and coefficient of determination (R2) for every possible combination. Any tip/idea/library/script how do to so. Thanks, As hz -- View thi

Re: [R] Linear regression equation and coefficient matrix

Hi, Thanks, the cor() works. Regarding the simple linear regression equation (mainly, the slope parameter) and r2. I think I was not writing it well. I need to do it just for the columns. If I have a, b, c, d columns I wish to compute the relation of there data, e.g., between a-b, a-c, a-d, b-a

[R] Correlograms and linear regression

Dear all, I generated a Correlograms and used the panel.ellipse (confidence ellipse and smoothed line) option. Is there a way to get instead of the smoothed line the linear regression? Thanks, As hz -- View this message in context: http://r.789695.n4.nabble.com/Correlograms-and-linear-regre

Re: [R] Linear regression equation and coefficient matrix

Dear Greg, Thanks for the tip. As I am new in R can you please provide me a script how do to so. It will help my learning process. Thanks, Asher -- View this message in context: http://r.789695.n4.nabble.com/Linear-regression-equation-and-coefficient-matrix-tp2329804p2330867.html Sent from the

[R] Scatterplot question

Hi, I have two XY datasets (e.g., longitude and concentrations) who share the same X scale. How can I make a simple scatterplot which will combine them both with different colors for the two Y groups? (plot and xyplot solutions are fine with me). Thanks in advance. Cheers -- View this messa

[R] lattice to ggplot2 conversion help

tion(x, y, type, ...) { panel.superpose(x, y, type="l", ...) lpoints(x, y, pch=16, col="white", cex=2) panel.superpose(x, y, type="p",...) }, par.settings = sp, auto.key = list(columns = 2, lines = TRUE))) I will be

[R] Time series and ggplot2

display all the months in the X axis text/labels? how can I display only January, April, July and October the months in the X axis text/labels? Thanks, Ashz PS axis.text.x = theme_text(angle=90) and scale_x_date(format = "%b-%Y") -- View this message in context: http://r.789695.n4.nabbl

[R] NA in last row while reading xlsx file

Hi, I am using this script to read a xlsx file to a data frame: library(xlsx) File <- file.path("d:", "car ", "car95-99.xlsx") B_car <- read.xlsx(File, "raw_data") Car2x <- data.frame(month = B_car$Date,Ch = B_car$Ch.des, lat=B_car$Latitude) The last row in the data.frame is always NA, how can I

[R] Scatter plots, linear regression in ggplot2

Hi, Based on some modification that I did to the R Cookbook Graphs Scatterplots code, link:http://wiki.stdout.org/rcookbook/Graphs/Scatterplots%20(ggplot2) I have some questions and I will appreciate a help: - How do I change the legend title? - How can I change the for each linear r

[R] Howto convert Linear Regression data to text

Dear all, How can I covert lm data to text in the form of "y=ax+b, r2" and how do I calculate R-squared(r2)? Thanks. Code: x=18:29 y=c(7.1,7,7.7,8.2,8.8,9.7,9.9,7.1,7.2,8.8,8.7,8.5) res=lm(y~x) -- View this message in context: http://r.789695.n4.nabble.com/Howto-convert-Linear-Regression-dat

[R] ggplot2-grid/viewport and PNG

Dear All, The following code save my graphs as pdf: pdf("j:/mix.pdf", width = 18, height = 16) grid.newpage() pushViewport(viewport(layout = grid.layout(3,1))) vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y) print(Aplot, vp = vplayout(1, 1)) print(Bplot, vp

[R] Simple R graph question

Dear All, I have several objects (imported from excel via using “xlsx”) with the field names: Month/Year, X, Y1, Y2, Y3. What is the best library/way to generate a graph which will be consist of multiple plots (Month/Year) that each contain the X, Y1, Y2, Y3 dataset. Thanks a lot. Cheers, Asher

Re: [R] Simple R graph question

Dear jholtman, Thanks for the reply & sorry for the been unclear before. My desire graph is to have multiply plots showing Y1,Y2,Y3 with the same X, were each plot is month-year (e.g., 5-2001, 6-2001, etc). It ill be great if each Y can have a different line and point style. The Lattice graph

[R] Fitting a Harmonic Function to Time Series Data

Dear All, I have some time series data where X=month and Y=nutrient concentration (I can have several concentration data for one month). Is there a way to fit for it an Harmonic Function. Is there a package, script,etc which I can use? Thx -- View this message in context: http://r.789695.n4.