similar to: Extract all point in a quadrats by spatstat package

Hi all, I am using quadratcount in spatstat to divide a window containing a point pattern into a grid of quadrats containing the intensity of points in each quadrat. My data is in UTM co-ordinates. My window is defined as follows: >p15<-ppp(x,y,window=owin(c(341710,342100),c(3126465,3126780)),marks=NUL L, checks=TRUE) Giving me a distance of 390m in the 'x' direction and 315m in

Try text(0.5, 0.5, label = "?text") On Sat, 10 Feb 2018, 16:22 Mohammad Tanvir Ahamed via R-help, < r-help at r-project.org> wrote: > Hi, > I want to label a polygon (circle or polygon) inside. > As for example code > > library(spatstat) > x <- runif(20) > y <- runif(20) > X <- ppp(x, y, window=disc(0.7)) > plot(X) > > Now I want to

Hi,? I want to label a polygon (circle or polygon) inside. As for example code? library(spatstat) x <- runif(20) y <- runif(20) X <- ppp(x, y, window=disc(0.7)) plot(X) Now I want to label that circle inside . Can some one please help me ?? Thanks.? Regards............. Tanvir Ahamed Stockholm, Sweden???? |??mashranga at yahoo.com

Hi, I know there are older threads discussing the quadratcount function in spatstat. Unfortunately, I could not find a solution to my problem there. I'm analyzing a point pattern in an irregular polygonal window. Both the window (an entire country) and the points are projected using WGS84. When I do quadratcount with only one quadrat for the entire country it holds all my 154 points:

Hi,?In your data file, the first row does not have an equal number of column like the rest of the row.Check your data file. Specially 1st row.?? Regards.............Tanvir Ahamed Stockholm, Sweden | mashranga at yahoo.com On Monday, 5 October 2020, 08:11:48 am GMT+2, Mir Md. Abdus Salam <mir.salam at uef.fi> wrote: Dear all, I need urgent help. I am a new user of R. I

Hi,? I have two big data set.? data _1 :? > dim(data_1) [1] 15820 5 > head(data_1) ? ?Chromosome ?????Start????????End????????Feature GroupA_3 1: ? ? ? ????????chr1 521369 ?750000 ????chr1-0001 ? ?????0.170 2: ? ? ? ????????chr1 750001 ?800000 ????chr1-0002 ? ????-0.086 3: ? ? ? ????????chr1 800001 ?850000 ????chr1-0003 ? ?????0.006 4: ? ? ? ????????chr1 850001 ?900000 ????chr1-0004 ?

Hi,? I have made violin plot with both ggplot2 and vioplot package with same data.? The results and code are as follows.? ################### ?Loading data? data.melt <- dget("https://gubox.box.com/shared/static/rirth0eym114afwyjxwe128sjzipzdym.txt") ################### ?Violin plot by library(vioplot) library(vioplot) data.use_11<- data.melt$value[data.melt$ident == 0]

Hi, Using the quadrats and quadratcount functions in spatstat, when I go to plot either of these, I get the quadrats coloured by their identity, i.e., using a color ramp applied to the sequence of quadrats. This only happens when the quadrats are applied to an owin which is polygonal, i.e., when I have an irregularly shaped study area. There doesn't seem to be any obvious way to

Hello, I am trying to plot a quadratcount object over a ppp object in the spatstat package. I ultimately want to get something like this http://bg9.imslab.co.jp/Rhelp/R-2.4.0/src/library/spatstat/man/images/big_quadratcount_001.png http://bg9.imslab.co.jp/Rhelp/R-2.4.0/src/library/spatstat/man/images/big_quadratcount_001.png See

I have photographs of plots that look like so: http://r.789695.n4.nabble.com/file/n4631960/Untitled.jpg I need to divide it up so each circle has an equal area surrounding it. So into 20 equal segments, each of which contains a circle. Quadratcount is not sufficient because if I divide it up into 36 equal quadrats, some quadrats do not contain one of the circles. I'm not even sure how to

Hi, I'm new to this mailing list so apologies if this is too basic. I have confocal images 512x512 from which I have extracted x,y positions of the coordiates of labelled cells exported from ImageJ as a.csv file. I also have images that define an underlying pattern in the tissue defined as areas of different pixel values 0 or 255 (also 512x512) I've exported these images as .txt

Hello R Users, I am trying to do a quadrat count defined by covariate properties in spatstat. I have read my elevation raster into R (from ascii) and converted to class "im" for use in spatstat. Now I have point data of class "ppp" which window is the same extent as the elevation image. I can conveniently plot the image and the points on the image as follows:

Hello R Users, I am trying to do a quadrat count defined by covariate properties in spatstat. I have read my elevation raster into R (from ascii) and converted to class "im" for use in spatstat. Now I have point data of class "ppp" which window is the same extent as the elevation image. I can conveniently plot the image and the points on the image as follows:

hi , this can be done easily if (cond) expr ex:  > for (i in 1: 4)+ {+ if(i==2) print("a")+ if(i==2) print("b")+ } output : [1] "a"[1] "b" but i want this  if (cond) expr1 expr 2 i tried this :  > for (i in 1: 4)+ {+ if(i==2) (print("b") && print("a"))+ } output : [1] "b"Error in print("b") &&

Hello everybody-- I have been playing with my data in spatstat, and what I'd like to present is a basic exploratory spatial analysis. I have used the following code, using a ppp.object called tsdspoints. The code develops the simulations and the envelopes I want, but I don't understand my first plot here, the [tsds.ghat.short$r, tsds.ghat.short$raw]...I cobbled together this code

Hi, I can run the code some days ago . But cant run now.  Problem 1: Output is ok ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl)  Output :                                                                                                5utr

Hi !  Facing problem with " getSequence" commend .  when only biomaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq) but when i have loaded the seqinr, i got problem

Hello all ,  I have a data frame like this  X1X2X3 11815 22916 331017 441118 551219 661320 771421 now i want to randomly reorder the variable X2  but the row element should be same  as for example  X1X2X3 12916 251219 331017 471421 561320 61815 741118 how can i do that ?? Hint :  this could be helpful :  if X2 is only a vector like this  X2<-c(8,9,10,11,12,13,14) so i can easily reorder

Dear All (probably Hadley), I am now trying to customise some plots using a bar geom. I do not want to use the default binning statistic, but rather calculate the bar heigths separately. I do manage this, but for comparison purposes I would like to have a set of plots all with the same y-axis height. But I do not seem to find out how to fix the scale of the y-axis in this case. Any tips?

I've written the function below to simulate the mean 1st through nth nearest neighbor distances for a random spatial pattern using the functions nndist() and runifpoint() from spatsat. It works, but runs relatively slowly - would appreciate suggestions on how to speed up this function. Thanks. --Dale library(spatstat) sim.nth.mdist <- function(nth,nsim) { D <- matrix(ncol=nth,