# 2 D density plot interpretation and manipulating the data

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## 2 D density plot interpretation and manipulating the data

 Hello, I have a data frame like this: > head(SNP)                mean      var     sd FQC.10090295 0.0327 0.002678 0.0517 FQC.10119363 0.0220 0.000978 0.0313 FQC.10132112 0.0275 0.002088 0.0457 FQC.10201128 0.0169 0.000289 0.0170 FQC.10208432 0.0443 0.004081 0.0639 FQC.10218466 0.0116 0.000131 0.0115 ... and I am creating plot like this: s <- ggplot(SNP, mapping = aes(x = mean, y = var)) s <- s +  geom_density_2d() + geom_point() + my.theme + ggtitle("SNPs") s I am getting plot in attach. My question is how do I: 1.interpret the inclusion versus exclusion within the ellipses-contours? 2. how do I extract from my data frame the points which are outside of ellipses? Thanks Ana ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. snps.pdf (37K) Download Attachment
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## Re: 2 D density plot interpretation and manipulating the data

 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 Qu.    Max.       0     383     696     738    1170    1789 where get_density() is function from here: https://slowkow.com/notes/ggplot2-color-by-density/and then do something like this: a=SNP[SNP\$density>400,] and plot it again: p <- ggplot(a, mapping = aes(x = mean, y = var)) p <- p +  geom_density_2d() + geom_point() + my.theme + ggtitle("SNPS_red") On Thu, Oct 8, 2020 at 3:52 PM Ana Marija <[hidden email]> wrote: > > Hello, > > I have a data frame like this: > > > head(SNP) >                mean      var     sd > FQC.10090295 0.0327 0.002678 0.0517 > FQC.10119363 0.0220 0.000978 0.0313 > FQC.10132112 0.0275 0.002088 0.0457 > FQC.10201128 0.0169 0.000289 0.0170 > FQC.10208432 0.0443 0.004081 0.0639 > FQC.10218466 0.0116 0.000131 0.0115 > ... > > and I am creating plot like this: > > s <- ggplot(SNP, mapping = aes(x = mean, y = var)) > s <- s +  geom_density_2d() + geom_point() + my.theme + ggtitle("SNPs") > s > > I am getting plot in attach. > > My question is how do I: > 1.interpret the inclusion versus exclusion within the ellipses-contours? > > 2. how do I extract from my data frame the points which are outside of ellipses? > > Thanks > Ana ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: 2 D density plot interpretation and manipulating the data

 > 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 *has* elliptical contours. A kernel density estimate is usually regarded as an estimate of an unknown density function. Often they use a normal (or Gaussian) kernel, but I wouldn't describe them as normal approximations. In general, bivariate kernel density estimates do *not* have elliptical contours. But in saying that, if the data is close to normality, then contours will be close to elliptical. Kernel density estimates do not test for inclusion, as such. (But technically, there are some exceptions to that). I'm not sure what you're trying to achieve here. ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: 2 D density plot interpretation and manipulating the data

 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 <- ggplot(SNP, mapping = aes(x = mean, y = var)) s <- s +  geom_density_2d() + geom_point() + my.theme + ggtitle("SNPs") versus what is in the data: > head(SNP)                mean      var     sd FQC.10090295 0.0327 0.002678 0.0517 FQC.10119363 0.0220 0.000978 0.0313 FQC.10132112 0.0275 0.002088 0.0457 FQC.10201128 0.0169 0.000289 0.0170 FQC.10208432 0.0443 0.004081 0.0639 FQC.10218466 0.0116 0.000131 0.0115 ... the distribution is not normal, it is right-skewed. Cheers, Ana On Fri, Oct 9, 2020 at 2:13 AM Abby Spurdle <[hidden email]> wrote: > > > 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 *has* elliptical contours. > > A kernel density estimate is usually regarded as an estimate of an > unknown density function. > Often they use a normal (or Gaussian) kernel, but I wouldn't describe > them as normal approximations. > In general, bivariate kernel density estimates do *not* have > elliptical contours. > But in saying that, if the data is close to normality, then contours > will be close to elliptical. > > Kernel density estimates do not test for inclusion, as such. > (But technically, there are some exceptions to that). > > I'm not sure what you're trying to achieve here. ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: 2 D density plot interpretation and manipulating the data

 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 trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Fri, Oct 9, 2020 at 8:25 AM Ana Marija <[hidden email]> wrote: > 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 <- ggplot(SNP, mapping = aes(x = mean, y = var)) > s <- s +  geom_density_2d() + geom_point() + my.theme + ggtitle("SNPs") > > versus what is in the data: > > > head(SNP) >                mean      var     sd > FQC.10090295 0.0327 0.002678 0.0517 > FQC.10119363 0.0220 0.000978 0.0313 > FQC.10132112 0.0275 0.002088 0.0457 > FQC.10201128 0.0169 0.000289 0.0170 > FQC.10208432 0.0443 0.004081 0.0639 > FQC.10218466 0.0116 0.000131 0.0115 > ... > > the distribution is not normal, it is right-skewed. > > Cheers, > Ana > > On Fri, Oct 9, 2020 at 2:13 AM Abby Spurdle <[hidden email]> wrote: > > > > > 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 *has* elliptical contours. > > > > A kernel density estimate is usually regarded as an estimate of an > > unknown density function. > > Often they use a normal (or Gaussian) kernel, but I wouldn't describe > > them as normal approximations. > > In general, bivariate kernel density estimates do *not* have > > elliptical contours. > > But in saying that, if the data is close to normality, then contours > > will be close to elliptical. > > > > Kernel density estimates do not test for inclusion, as such. > > (But technically, there are some exceptions to that). > > > > I'm not sure what you're trying to achieve here. > > ______________________________________________ > [hidden email] mailing list -- To UNSUBSCRIBE and more, see > 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. >         [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: 2 D density plot interpretation and manipulating the data

 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 11:31 AM Bert Gunter <[hidden email]> wrote: > > 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 trouble with having an open mind is that people keep coming along and sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Fri, Oct 9, 2020 at 8:25 AM Ana Marija <[hidden email]> wrote: >> >> 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 <- ggplot(SNP, mapping = aes(x = mean, y = var)) >> s <- s +  geom_density_2d() + geom_point() + my.theme + ggtitle("SNPs") >> >> versus what is in the data: >> >> > head(SNP) >>                mean      var     sd >> FQC.10090295 0.0327 0.002678 0.0517 >> FQC.10119363 0.0220 0.000978 0.0313 >> FQC.10132112 0.0275 0.002088 0.0457 >> FQC.10201128 0.0169 0.000289 0.0170 >> FQC.10208432 0.0443 0.004081 0.0639 >> FQC.10218466 0.0116 0.000131 0.0115 >> ... >> >> the distribution is not normal, it is right-skewed. >> >> Cheers, >> Ana >> >> On Fri, Oct 9, 2020 at 2:13 AM Abby Spurdle <[hidden email]> wrote: >> > >> > > 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 *has* elliptical contours. >> > >> > A kernel density estimate is usually regarded as an estimate of an >> > unknown density function. >> > Often they use a normal (or Gaussian) kernel, but I wouldn't describe >> > them as normal approximations. >> > In general, bivariate kernel density estimates do *not* have >> > elliptical contours. >> > But in saying that, if the data is close to normality, then contours >> > will be close to elliptical. >> > >> > Kernel density estimates do not test for inclusion, as such. >> > (But technically, there are some exceptions to that). >> > >> > I'm not sure what you're trying to achieve here. >> >> ______________________________________________ >> [hidden email] mailing list -- To UNSUBSCRIBE and more, see >> 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. ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: 2 D density plot interpretation and manipulating the data

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