[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 <- princomp(data1[,1:4], score=TRUE, cor=TRUE)
biplot(pca1)
The biplot present the data points as numbers. How can I present the data
point in color (depends on their group-column 5). I was thinking about doing
it using ggplot2 but I can not succeed. Any idea how to do it?
Thanks
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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 right, how can I implement my data.frames?
Thanks again
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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$coord[,1], pca$ind$coord[,2], colour = dat1$item)) + geom_point() + theme(legend.position="none") I still do not get separation by color by group (column 5 of csv file) as the dat1 is empty (data frame with 0 columns and 0 rows). Any reason why? Thanks again. -- View this message in context: http://r.789695.n4.nabble.com/PCA-and-gglot2-tp4671225p4671253.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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.scale = 1,groups = my.class,
ellipse = TRUE, circle = TRUE)
g <- g + scale_color_discrete(name = '')
g <- g + theme(legend.direction = 'horizontal',
legend.position = 'top')
print(g)
BTW
Installation:
library(devtools)
install_github("ggbiplot", "vqv")
you will need to instal before Rtools
(http://cran.r-project.org/bin/windows/Rtools/)
Thanks a lot for the help.
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[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-in-lda-MASS-tp4673696.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 this message in context: http://r.789695.n4.nabble.com/Image-Gray-Level-Co-occurrence-Matrix-in-R-tp4670401.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 + Petal.Length + Petal.Width, data = iris) LD1<-predict(iris.lda)$x[,1] LD2<-predict(iris.lda)$x[,2] ggplot(iris, aes(x=LD1, y=LD2, col=iris$Species) ) + geom_point( size = 4, aes(color = iris$Species))+theme_bw() -- View this message in context: http://r.789695.n4.nabble.com/Mark-each-group-centroid-in-a-linear-discriminant-analysis-plot-tp4680159.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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, 0.123456789), digits=digits)[1]
txt = paste(prefix, txt, sep="")
if(missing(cex.cor)) cex.cor = 0.8/strwidth(txt)
text(0.5, 0.5, txt, cex = cex.cor)
}
pairs(ap[8:11], lower.panel=panel.smooth, upper.panel=panel.cor)
My question is how I can change the lower.panel to show both the pearson
linear correlation and Density Ellipse?
Thanks a lot.
As Hz
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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.complete.obs method for the upper.panel. Can it be fixed? - Can I remove the histograms? - Can I control the eliipse alpha? Thanks a lot. -- View this message in context: http://r.789695.n4.nabble.com/Scatterplot-matrix-Pearson-linear-correlation-and-Density-Ellipse-tp2763552p2953521.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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]
txt = paste(prefix, txt, sep="")
if(missing(cex.cor)) cex.cor = 0.8/strwidth(txt)
text(0.5, 0.5, txt, cex = cex.cor)
}
pairs(cap[8:11], lower.panel=panel.lm, upper.panel=panel.cor, cex=2)
I get linear regression and density ellipse, why?
Is it possible to add also the data point?
Thanks a lot
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[R] Xlsx and R -read problem
Hi,
I have an excel 2007 file located in C:\know and called try.xlsx.
Whan I try to read it I get this error:
> file <- system.file("know", "try.xlsx", package = "xlsx")
> res <- read.xlsx(file, 2) # read the second sheet
Error in .jnew("java/io/FileInputStream", file) :
java.io.FileNotFoundException:
Can someone tell me what is the problem? and how to solve it.
Cheers,
Ashz
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[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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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-deviation-tp3001683p3001683.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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/points-x-y-mean-and-standard-deviation-tp3001683p3002173.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 - Y2 and Y1 + Y2 halistat$Date values: 29/1/10 21/2/10 30/3/10 30/4/10 30/5/10 In the resulted plot the X values are sorted, how can I cancel it? Thanks. -- View this message in context: http://r.789695.n4.nabble.com/ggplot-unwanted-sorted-X-values-tp3015099p3015099.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ggplot output
Dear All, I have this script: dat <- data.frame(Month = hstat$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$Date,K_avg = hstat$K.avg,K_stdev = hstat$K.stdev) ggplot(data = dat, aes(x = Month, y = K_avg, ymin = K_avg - K_stdev, ymax = K_avg + K_stdev)) + geom_point() + geom_line() + geom_errorbar() dat <- data.frame(Month = hstat$Date,S_avg = hstat$S.avg,S_stdev = hstat$S.stdev) ggplot(data = dat, aes(x = Month, y = S_avg, ymin = S_avg - S_stdev, ymax = S_avg + S_stdev)) + geom_point() + geom_line() + geom_errorbar() Running the script generates 3 separate graphs, how can I output them next to each other? Thanks -- View this message in context: http://r.789695.n4.nabble.com/ggplot-output-tp3027026p3027026.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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://r.789695.n4.nabble.com/Automated-plot-and-linear-regression-line-data-tp2328027p2328027.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 this message in context: http://r.789695.n4.nabble.com/Linear-regression-equation-and-coefficient-matrix-tp2329804p2329804.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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, b-c, b-d, etc. I hope it is clear now and an help will be great. Thanks. -- View this message in context: http://r.789695.n4.nabble.com/Linear-regression-equation-and-coefficient-matrix-tp2329804p2329948.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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-regression-tp2331071p2331071.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
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 help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 message in context: http://r.789695.n4.nabble.com/Scatterplot-question-tp2341456p2341456.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lattice to ggplot2 conversion help
Hi,
I am interested in ggplot2 and I found this lattice code very interesting
(http://addictedtor.free.fr/graphiques/graphcode.php?graph=48).
Code:
library(lattice)
lattice.options(default.theme = canonical.theme(color = FALSE))
tmp <-
expand.grid(geology = c("Sand","Clay","Silt","Rock"),
species = c("ArisDiff", "BracSera", "CynDact",
"ElioMuti", "EragCurS", "EragPseu"),
dist = seq(1,9,1) )
tmp$height <- rnorm(216)
sp <- list(superpose.symbol = list(pch = 1:6, cex = 1.2),
superpose.line = list(col = "grey", lty = 1))
# print is needed when you source() the file
print(xyplot(height ~ dist | geology, data = tmp,
groups = species,
layout = c(2,2),
panel = function(x, y, type, ...) {
panel.superpose(x, y, type="l", ...)
lpoints(x, y, pch=16, col="white", cex=2)
panel.superpose(x, y, type="p",...)
},
par.settings = sp,
auto.key = list(columns = 2, lines = TRUE)))
I will be very happy if someone can please explain me how to do it in
ggplot2 as it will be great help.
Cheers,
Ashz
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[R] Time series and ggplot2
Hi, I made a time-series plot using ggplot. All the points are shown in the graph but unfortunately it does not display all the months in the graph X-axis text/labels but only one month per year. Furthermore, the data contain some NA as not all the month as Y values. Therefore, how can I display all the months in the X axis text/labels? how can I display only January, April, July and October the months in the X axis text/labels? Thanks, Ashz PS axis.text.x = theme_text(angle=90) and scale_x_date(format = "%b-%Y") -- View this message in context: http://r.789695.n4.nabble.com/Time-series-and-ggplot2-tp3761434p3761434.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] NA in last row while reading xlsx file
Hi,
I am using this script to read a xlsx file to a data frame:
library(xlsx)
File <- file.path("d:", "car ", "car95-99.xlsx")
B_car <- read.xlsx(File, "raw_data")
Car2x <- data.frame(month = B_car$Date,Ch = B_car$Ch.des,
lat=B_car$Latitude)
The last row in the data.frame is always NA, how can I remove it?
Thx.
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[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 regression its color and linetype?
- How can I add for both the linear regression lines their equations and
Rseq inside or below the plot?
Code:
set.seed(955)
df <- data.frame(cond = rep(c('A', 'B'), each=10),
xvar = 1:20 + rnorm(20,sd=3),
yvar = 1:20 + rnorm(20,sd=3))
ggplot(df, aes(x=xvar, y=yvar, shape=cond)) +
scale_shape_manual(values=c(1,2)) +
geom_smooth(method = "lm", se=FALSE) +
theme_bw()+
geom_point(size = 5)+
opts(title = "Xvar vs. Yvar",
plot.title = theme_text(face="bold", size=16),
axis.text.x = theme_text(angle=90),
axis.title.x = theme_text(face="bold", size=12),
axis.title.y = theme_text(face="bold", size=12, angle=90),
panel.grid.major = theme_blank(), # switch off major gridlines
panel.grid.minor = theme_blank()
)
Thanks a lot in advance
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vplayout <- function(x, y)
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print(Aplot, vp = vplayout(1, 1))
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dev.off()
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Thanks
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