search for: snps_red

...ity() is function from here: https://slowkow.com/notes/ggplot2-color-by-density/ and keep only entries with density > 400 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") and probably I can increase that threshold... Any idea how do I interpret data points that are left contained within the ellipses? On Fri, Oct 9, 2020 at 6:09 PM Abby Spurdle <spurdle.a at gmail.com> wrote: > > You could assign a density value to each point. > Maybe you'...

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

...re 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 <sokovic.anamarija at gmail.com> 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 0.03...

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))