[BioC] flowviz

Tue Aug 12 20:16:34 CEST 2014

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
>>>>>> Permoserstraße 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
>>>>> Permoserstraße 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
>>> Permoserstraße 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
> Permoserstraße 15, 04318 Leipzig
>
> E-Mail:joachim.schumann at ufz.de  
> http://www.ufz.de  

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