Question: flowviz
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gravatar for Jiang, Mike
5.2 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:
`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 >>> >> > >
flowviz • 759 views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Jiang, Mike1.2k
Answer: flowviz
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gravatar for Jiang, Mike
5.2 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:
'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├če 15, 04318 Leipzig >> >> E-Mail: joachim.schumann@ufz.de >> http://www.ufz.de >> > -- > Joachim Schumann > Department of Environmental Microbiology > AG Flow Cytometry > Helmholtz Centre for Environmental Research - UFZ > Permoserstra├če 15, 04318 Leipzig > E-Mail: joachim.schumann@ufz.de <mailto:joachim.schumann@ufz.de> > http://www.ufz.de [[alternative HTML version deleted]]
ADD COMMENTlink written 5.2 years ago by Jiang, Mike1.2k
Answer: flowviz
0
gravatar for Jiang, Mike
5.2 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:
All the graphical parameters can be set through lattice/Trellis settings: ' par.settings'. e.g. to set background color, simply do: xyplot(`SSC-H`~`FSC-H`, fs, par.settings = list(panel.background=list(col = "white"))) to remove grid, xyplot(`SSC-H`~`FSC-H`, fs, axis = axis.default) Also 'trellis.par.get()` will give you the full list of lattice graphical parameters. Mike On 03/26/2014 03:27 AM, Joachim Schumann wrote: > Can I change the color of the background within the xyplot? Now it's > grey but I would change it into white (I don't need the grids). > > Joachim
ADD COMMENTlink written 5.2 years ago by Jiang, Mike1.2k
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