To construct 'rectangleGate' programmatically, you can use '.gate' argument: definition = function(channel1="FS.Log",channel2="FL.4.Log",x_start=500,x_end=3500, y_start=500,y_end=3000,...) { coords <- list(c(x_start,x_end), c(y_start,y_end)) names(coords) <- c(channel1, channel2) Noise <- rectangleGate(filterId="Noise", .gate = coords) } Mike On 09/02/2014 07:00 AM, Joachim Schumann wrote: > Hi Mike, > > thanks, that woks great. Now, I'm having a little problem. After > reading a fcs file I want to use the method > rectangleGate(). > > To define the channels I use e.g. > > Noise <- rectangleGate(filterId="Noise", list("FS.Log"=c(500,3500), > "FL.4.Log"=c(500,3000))) > > But my own method has the parameters channel1 and channel2, e.g. > definition = > function(channel1="FS.Log",channel2="FL.4.Log",x_start=500,x_end=350 0,y_start=500,y_end=3000,...) > > Writing the following: > > Noise <- rectangleGate(filterId="Noise", > list(channel1=c(x_start,x_end), channel2=c(y_start,y_end))) > > does not work. > > How can I use both parameters (channel1,channel2) within the > rectangleGate method so that the user can define which channels he > wants to use? > > Best, > Joachim > > Am 12.08.2014 20:16, schrieb Mike: >> Joachim, >> >> Sorry I misunderstood your problem. It is probably not easy to do so >> unless you are willing to hack into hexbin::grid.hexagons and >> flowViz::panel.xyplot.flowframe. >> >> If it is just for small data set, you can simply use bin the data and >> do ggplot on the data.frame ,which gives you more flexibility in >> coloring. >> Here is one example: >> >> library(ggplot2) >> mat<-exprs(fs[[1]]) >> x<- mat[,"FSC-H"] >> y<- mat[,"SSC-H"] >> bin <- hexbin(x,y, xbin = 128) >> df <- data.frame(hcell2xy(bin), count = bin at count) >> ggplot(df, aes(x = x, y = y)) + geom_point(aes(color = sqrt(count))) >> + scale_color_gradient(low = "white", high = "black" , na.value = >> "red", limit = c(1, 2)) + theme_bw() >> >> >> Yon change use the 'limit' and 'na.value' to thresholding the colors. >> >> Mike >> >> >> >> Mike >> On 08/12/2014 05:42 AM, Joachim Schumann wrote: >>> Hi Mike, >>> >>> I did not get the point how to write a color ramp function with a >>> treshold. >>> >>> Right now I'm creating the xyplots like that: >>> >>> ff<-read.FCS("test.fcs",alter.names=TRUE,transformation=FALSE,min. limit=NULL) >>> colramp <- colorRampPalette(c("white","black"))(236) >>> col=colorRampPalette(colramp) >>> xyplot(FS.Log ~ FL.4.Log ,data=ff, smooth=FALSE, xbin=128, >>> colramp=col ,par.settings = list(panel.background=list(col = >>> "white")), axis = axis.default, scales=(list(x=list(draw=FALSE), >>> y=list(draw=FALSE))), xlab="", ylab="") >>> >>> I can get the maximal value by: >>> >>> mat<-exprs(ff) >>> x<-mat[,"FS.Log"] >>> y<-mat[,"FL.4.Log"] >>> bin<-hexbin(x,y,xbins=128) >>> c<-bin at count >>> m<-max(c) >>> >>> The counts should be the values plotted by the xyplot function, right? >>> >>> How can I define the color palette with 236 linear gradiations from >>> white to black starting by 0, ending by e.g. m-100. All the other >>> values (m-100 to m) shall be black. >>> >>> Thank. >>> >>> Joachim >>> >>> Am 24.03.2014 18:34, schrieb Mike: >>>> >>>> If you use |hexbin| version of |xyplot|, then the value is simply >>>> the cell counts falling into each hexagon. >>>> It is not difficult to write your own customized colour ramp >>>> function to generate color schemes that you described based on your >>>> threshold. >>>> >>>> There are a little hacking you need to do in order to get the count >>>> value of each hexagon though, firstly you need to call |hexbin| on >>>> each |flowFrame|, >>>> >>>> |bin <- hexbin(x,y,xbins=xbins) >>>> | >>>> >>>> |x, y| is the intensity values from the two channels you defined in >>>> formula (e.g. |SSC-H|~|FSC-H|), which you can get by >>>> >>>> |mat <- exprs(fs[[1]]) >>>> x <- mat[, channel_A) >>>> y <- mat[, channel_B) >>>> | >>>> >>>> then you get the the counts vector by |bin at count|. >>>> >>>> Mike >>>> >>>> On 03/22/2014 03:44 AM, Joachim Schumann wrote: >>>> >>>>> Hi Mike, >>>>> >>>>> thanks for your answer. I defined a colramp from white to black >>>>> now. Is there any way I can have a look at the values that are >>>>> calculated within the xyplot? The reason: I want to define a >>>>> threshold. E.g.: The highest value within the xyplot is 1000, the >>>>> lowest is 0. I want all values ranging from 900-1000 beeing black >>>>> and all values from 900-0 should have those 255 gradiations. >>>>> >>>>> Best, >>>>> Joachim >>>>> >>>>> Am 20.03.2014 19:04, schrieb Mike: >>>>>> 'colramp' argument is what you are looking for, here is the >>>>>> example code. >>>>>> >>>>>> library(flowViz) >>>>>> data(GvHD) >>>>>> fs <- GvHD[1:2] >>>>>> >>>>>> #generate all colors you need >>>>>> myColors <- gray.colors(255) >>>>>> #reverse it as you want dark for high and white for low >>>>>> myColors <- rev(myColors) >>>>>> #wrap it into a ramp function >>>>>> myColRamp <- colorRampPalette(myColors) >>>>>> >>>>>> # pass the ramp function to xyplot >>>>>> xyplot(`SSC-H`~`FSC-H`, fs, smooth = FALSE, xbin = 128, colramp = >>>>>> myColRamp) >>>>>> >>>>>> >>>>>> Mike Jiang >>>>>> >>>>>> On 03/18/2014 09:34 AM, Joachim Schumann wrote: >>>>>>> Hi Mike, >>>>>>>> >>>>>>>> thanks for your answer. I think xbin is the only thing I need. >>>>>>>> But I >>>>>>>> have another question: I want to create a xyplot of my data. >>>>>>>> The range >>>>>>>> of e.g. columns FS.Log and FL.4.Log is from 0-4095. I want to >>>>>>>> display >>>>>>>> the xyplot (FL.4.Log ~ FS.Log) as a grayscale image with 256 linear >>>>>>>> gradiations. Black should indicate 4095 (maxRange) and white should >>>>>>>> indicate 0 (minRange). Now I need 256 linear gradiations from >>>>>>>> black to >>>>>>>> white. The data resolution should be 128. >>>>>>>> Can you tell me how to create such a grayscale image? I attached an >>>>>>>> image showing the grayscale. >>>>>>>> >>>>>>>> Best, >>>>>>>> Joachim >>>>>>>> >>>>>>>> >>>>>>>> Am 14.03.2014 18:07, schrieb Mike: >>>>>>>> > `nbin` is for displaying the marginal events (i.e. those gray >>>>>>>> segments >>>>>>>> > piled up at the edges) >>>>>>>> > >>>>>>>> > `binSize` is for `timeline plotting`, i.e. when you do >>>>>>>> 'xyplot' on a >>>>>>>> > `flowFrame` without 'formula` supplied , for example: >>>>>>>> > >>>>>>>> > xyplot(GvHD[["s5a05"]], binSize = 100) >>>>>>>> > >>>>>>>> > So again, 'xbin' is the argument to adjust the 'resolution' for >>>>>>>> > 'non-smoothed' xyplot . e.g. >>>>>>>> > >>>>>>>> > xyplot(`FSC-H` ~ `SSC-H`, GvHD[["s5a05"]], smooth = FALSE, >>>>>>>> xbin = 32) >>>>>>>> > #lower resolution and faster rendering >>>>>>>> > >>>>>>>> > xyplot(`FSC-H` ~ `SSC-H`, GvHD[["s5a05"]], smooth = FALSE, >>>>>>>> xbin = 128) >>>>>>>> > #higher resolution and slower rendering >>>>>>>> > >>>>>>>> > >>>>>>>> > Mike >>>>>>>> > >>>>>>>> > >>>>>>>> > On 03/13/2014 04:08 AM, Joachim Schumann wrote: >>>>>>>> >> Yes, i meant the xyplot. Can I also change the number of events >>>>>>>> >> within one bin? The vignette sometimes says nbin, sometimes >>>>>>>> binSize. >>>>>>>> >> >>>>>>>> >> Am 12.03.2014 18:11, schrieb Mike: >>>>>>>> >>> Not sure what you mean by `histogram`. If you are talking about >>>>>>>> >>> `xyplot`, there is `xbin` argument to adjust resolution >>>>>>>> (when you >>>>>>>> >>> set `smooth = FALSE`). >>>>>>>> >>> >>>>>>>> >>> Mike >>>>>>>> >>> On 03/12/2014 05:32 AM, Joachim Schumann wrote: >>>>>>>> >>>> Hi Mr. Jiang, >>>>>>>> >>>> >>>>>>>> >>>> I'm using flowViz to create a histogram of my flow >>>>>>>> cytometric data. >>>>>>>> >>>> Is there any way I can adjust the data resolution (eg to 128) >>>>>>>> >>>> within the histogram? >>>>>>>> >>>> >>>>>>>> >>>> Best regards, >>>>>>>> >>>> Joachim >>>>>>>> >>>> >>>>>>>> >>> >>>>>>>> >> >>>>>>>> >> >>>>>>>> > >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> M. Sc. Joachim Schumann >>>>>>>> Department of Environmental Microbiology >>>>>>>> AG Flow Cytometry >>>>>>>> Helmholtz Centre for Environmental Research - UFZ >>>>>>>> Permoserstra?e 15, 04318 Leipzig >>>>>>>> >>>>>>>> E-Mail: joachim.schumann at ufz.de >>>>>>>> http://www.ufz.de >>>>>>>> >>>>>>> -- >>>>>>> Joachim Schumann >>>>>>> Department of Environmental Microbiology >>>>>>> AG Flow Cytometry >>>>>>> Helmholtz Centre for Environmental Research - UFZ >>>>>>> Permoserstra?e 15, 04318 Leipzig >>>>>>> E-Mail: joachim.schumann at ufz.de <mailto:joachim.schumann at="" ufz.de=""> >>>>>>> http://www.ufz.de >>>>>> >>>>> >>>>> >>>>> -- >>>>> M. Sc. Joachim Schumann >>>>> Department of Environmental Microbiology >>>>> AG Flow Cytometry >>>>> Helmholtz Centre for Environmental Research - UFZ >>>>> Permoserstra?e 15, 04318 Leipzig >>>>> >>>>> E-Mail:joachim.schumann at ufz.de >>>>> http://www.ufz.de >>> >>> >>> -- >>> M. Sc. Joachim Schumann >>> Department of Environmental Microbiology >>> AG Flow Cytometry >>> Helmholtz Centre for Environmental Research - UFZ >>> Permoserstra?e 15, 04318 Leipzig >>> >>> E-Mail:joachim.schumann at ufz.de >>> http://www.ufz.de >> > > > -- > M. Sc. Joachim Schumann > Department of Environmental Microbiology > AG Flow Cytometry > Helmholtz Centre for Environmental Research - UFZ > Permoserstra?e 15, 04318 Leipzig > Tel.: 0049-341-235-1330 > E-Mail:joachim.schumann at ufz.de > http://www.ufz.de [[alternative HTML version deleted]]