similar to: 2 D density plot interpretation and manipulating the data

You could assign a density value to each point. Maybe you've done that already...? Then trim the lowest n (number of) data points Or trim the lowest p (proportion of) data points. e.g. Remove the data points with the 20 lowest density values. Or remove the data points with the lowest 5% of density values. I'll let you decide whether that is a good idea or a bad idea. And if it's a

Hi Abby, Thanks for getting back to me, yes I believe I did that by doing this: SNP$density <- get_density(SNP$mean, SNP$var) > summary(SNP$density) Min. 1st Qu. Median Mean 3rd Qu. Max. 0 383 696 738 1170 1789 where get_density() is function from here: https://slowkow.com/notes/ggplot2-color-by-density/ and keep only entries with density > 400

I recommend that you consult with a local statistical expert. Much of what you say (outliers?!?) seems to make little sense, and your statistical knowledge seems minimal. Perhaps more to the point, none of your questions can be properly answered without subject matter context, which this list is not designed to provide. That's why I believe you need local expertise. Bert Gunter "The

Hi Abby, thank you for getting back to me and for this useful information. I'm trying to detect the outliers in my distribution based of mean and variance. Can I see that from the plot I provided? Would outliers be outside of ellipses? If so how do I extract those from my data frame, based on which parameter? So I am trying to connect outliers based on what the plot is showing: s <-

Hi Bert, Another confrontational response from you... You might have noticed that I use the word "outlier" carefully in this post and only in relation to the plotted ellipses. I do not know the underlying algorithm of geom_density_2d() and therefore I am having an issue of how to interpret the plot. I was hoping someone here knows that and can help me. Ana On Fri, Oct 9, 2020 at

> My understanding is that this represents bivariate normal > approximation of the data which uses the kernel density function to > test for inclusion within a level set. (please correct me) You can fit a bivariate normal distribution by computing five parameters. Two means, two standard deviations (or two variances) and one correlation (or covariance) coefficient. The bivariate normal

My understanding is that this represents bivariate normal approximation of the data which uses the kernel density function to test for inclusion within a level set. (please correct me) In order to exclude the outlier to these ellipses/contours is it advisable to do something like this: SNP$density <- get_density(SNP$mean, SNP$var) > summary(SNP$density) Min. 1st Qu. Median Mean 3rd

The blowfish crypt(3) mechanism supports the use of a "cost value" for password encryption. The cost value is encoded into the encrypted password that is stored in master.passwd. On OpenBSD, this cost value can be set in login.conf. FreeBSD does not currently support the cost value. The cost value is the base-2 logarithm of the number of rounds of encryption to use so

Hi Instead of ... ggsave("test_plot_chinese.pdf", m2) ... try ... cairo_pdf("test_plot_chinese.pdf") print(m2) dev.off() Paul On 13/10/17 02:12, John wrote: > I install the Chinese font "Kaiti TC" on my mac, but I can't print the > figures to pdf file by "marrangeGrob" command, which is in the package > "gridExtra". Error message

Hi By the looks of it, you need to install Cairo graphics ... https://www.cairographics.org/download/ Paul On 13/10/17 15:48, John wrote: > Thanks, Paul. Following your solution, ?I got this error message: > > Warning message: > In cairo_pdf("test_plot_chinese.pdf") : failed to load cairo DLL > > Is there anything else I need to install? > > Thanks, >

I install the Chinese font "Kaiti TC" on my mac, but I can't print the figures to pdf file by "marrangeGrob" command, which is in the package "gridExtra". Error message after I type "ggsave(......)" (last line of the program): "Saving 7.47 x 5.15 in image Error in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y, : invalid font

Thanks, Paul. Following your solution, I got this error message: Warning message: In cairo_pdf("test_plot_chinese.pdf") : failed to load cairo DLL Is there anything else I need to install? Thanks, John 2017-10-12 19:24 GMT-07:00 Paul Murrell <paul at stat.auckland.ac.nz>: > Hi > > Instead of ... > > ggsave("test_plot_chinese.pdf", m2) > > ...

Hi, Following Paul's instruction, I have installed the Cairo. I tried to run the program, and there is no error message at all. I did see the Chinese title in the plot if I ask my RStudio to show the plot (if I type "p1"), but the pdf file shows the plots without the Chinese titles. library(ggplot2) library(gridExtra) df1<-data.frame(x=1:2, y=3:4, z=5:6) #p1<-ggplot(df1,

Hi, Sorry to bother you with this question here. I tried to install Macports on my Mac OS Sierra, and type "sudo port install cairo", but it did not respond. I haven't seen any file name or app called Macports, but one file called "port" which is located at loca/bin/port" How should I do it? Thanks, John ******* Last login: Sun Oct 15 02:52:49

Hola a todos Me gustaría saber si me pueden ayudar con lo siguiente. Realicé un Boxplot usando ggplot2 para visualizar el comportamiento de dos variables. Visualmente no se notan las diferencias porque la gráfica de la derecha (parásitos en el abdomen) llega hasta 20 en el eje y. ¿Cómo puedo hacer para que las dos gráficas muestren la misma escala en el eje Y, es decir, que las dos lleguen a 60?

I have a function: myplot <- function (X) { d <- plotCounts(dds2, gene=X, intgroup="condition", returnData=TRUE) png(paste("img/", X, ".png", sep="")) ggplot(d, aes(x=condition, y=count, color=condition)) + geom_point(position=position_jitter(w=0.1,h=0)) + scale_y_log10(breaks=c(25,100,400)) + ggtitle(X) +

Hi, I'm using the gridExtra package to combine some graphs like in the arrangeGrob example. Each of the graphs has a title but they appear much larger than the overall combined plot title and left axis label. Does anyone know how I can control the style / size of the gridExtra labels? library(gridExtra) library(ggplot2) dsamp <- diamonds[sample(nrow(diamonds), 1000), ] p1 <-

I don't really understand. I mean, I understand the solution is print(ggplot(...)). But why is that required in a function and not at the console? Shouldn't I be able to rely on what I do at the console working in a script? Is this inconsistent behavior by design? On Thu, Nov 2, 2017 at 11:54 AM, David Winsemius <dwinsemius at comcast.net> wrote: > >> On Nov 2, 2017,

Hello, I am trying to add a less than equal to symbol in a ggplot2 legend text. See sample code below. I have tried using the expression function and \u2264. I also tried adding labels to legend.text under theme. Neither of these 3 options work. Please help, Mahesh ++++++++++++++ Extra.column=ifelse(data[,covariate]>cutpoint,1,0) Grp1 <- "\u2264 1.5" Grp2 <-

Hi, # For publications, I am not allowed to repeat the axes. I have tried to remove the axes using: # yaxt="n", but it did not work. I have not understood how to do this in ggplot2. Can you help me? # I also do not want loads of space between the graphs (see below script with Dummy Data). # If I could make it look like the examples on the (nice) examples page: #