[BioC] FlowViz graphics problems
Anja Schiel
anja.schiel at medisin.uio.no
Thu May 21 16:47:56 CEST 2009
Dear Deepayan,
Thanks a lot for your help! I very much appreciate that you take the
time to help me. Bellow some comments and another question, if you have
time.....
On Wed, 2009-05-20 at 14:13 -0700, Deepayan Sarkar wrote:
> On Wed, May 20, 2009 at 6:06 AM, Anja Schiel <a.e.schiel at medisin.uio.no> wrote:
> > Hi,
> >
> > I am currently testing flowCore and flowViz and have encountered some
> > problems.
> >
> > I am running :
> > R version 2.9.0 (2009-04-17)
> > i486-pc-linux-gnu
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods
> > base
> >
> > other attached packages:
> > [1] flowViz_1.8.0 lattice_0.17-25 flowCore_1.10.0 rrcov_0.5-01
> > [5] pcaPP_1.6 mvtnorm_0.9-5 robustbase_0.4-5 Biobase_2.4.1
> >
> > loaded via a namespace (and not attached):
> > [1] feature_1.2.3 graph_1.22.2 grid_2.9.0
> > KernSmooth_2.22-22
> > [5] ks_1.6.3 latticeExtra_0.5-4 MASS_7.2-47
> > RColorBrewer_1.0-2
> > [9] stats4_2.9.0 tools_2.9.0
> >
> >
> > I have noticed that when I use
> > xyplot(`SSC-H` ~ `FSC-H`, data = fs.trans[[1]], filter = eGate)
> > I get a plot with the Gate defined by eGate plotted, but when I try to
> > do the same with
> > flowPlot(fs.trans[[1]], filter = eGate)
> > the gate is not drawn. Since the default settings seem to be filter =
> > NULL (and I pass eGate to filter) and showFilter = TRUE I am wondering
> > if this is a glinch in the system or if my command is wrong.
>
> The 'flowPlot' function is not really maintained any more; the method
> for "flowFrame" does have a 'filter' argument, but it is never used in
> the actual function definition. xyplot() should be able to do
> everything flowPlot does. If not, please let us know.
>
> > Second I am somewhat confused about the plot function. When I transform
> > my FL-H signals with
> > fs.trans <- transform('FL1-H' = asinh, 'FL2-H' = asinh) %on% fs
> > and then run
> > plot (fs.trans[[7]], 'FL1-H', breaks=256)
> > I get a histogram with all my data crammed into the left corner due to
> > the y-axis scale that seems to be extremely large.
>
> The following seems to work for me:
>
> data(GvHD)
> fs <- GvHD
> fs.trans <- transform('FL1-H' = asinh, 'FL2-H' = asinh) %on% fs
> plot(fs[[7]], "FL1-H") ## most of the data in left-most bin
> plot(fs.trans[[7]], "FL1-H") ## much more spread out
>
> So we need a reproducible example to figure out why you are seeing
> different behavior.
>
It seems that my original FACS data must be different than the one used
for GvHD. I do see a relatively normal histogram with the GvHD data set,
as you point out. But when I use my own files the y-axis is set to 30
000 and not like in the example to 3000.
By the way, the problem becomes more obvious if I actually set the
breaks. If i set the breaks=256 then my graph gets extremely 'small', if
I do the same with the GvHD the effect is not the same.
I have attached 3 png files to show you what I get.
I could sent you some of my original files (like one with no signal in
FL1-H and one with a signal), but I am not sure if I can just attach
those to an e-mail. Maybe I can sent you an zip archive?
> > Also the axis changes
> > between the files. I have tried to figure out how this function works
> > (checked the normal and lattice information), but I am clearly not
> > understanding what is the underlying set of data points that determines
> > the y-axis scale. I would like to know how to reduce the y-axis scale
> > and keep it constant between different files (at least if this is not
> > something totally stupid to try).
>
> I'm not sure what you mean. Different calls with different flow frames
> will have different scales, based on the data for that frame. You
> should be able to explicitly specify 'xlim' and 'ylim' to be the same
> in all calls. This doesn't work now, and that's a bug. We will fix it
> soon.
>
Well that is related to the problem above. I tried to pass xlim and ylim
to the plot but nothing happened. I didn't get an error message either
so I thought I was doing it wrong (but if I define xlim and ylim in
xyplot it does work). So I was a bit confused. But if it is a bug then
in theory what I tried was correct and once it is fixed it should work.
In principal my idea was that I could just force the scale to be smaller
on the plot to make my data look better. It might also be necessary if I
need files for presentations or publications as it is usually expected
that all axis are of the same scale.
> You could always use densityplot() instead to compare multiple FCS files.
>
> densityplot(~`FL1-H` | names, data = fs.trans[1:5])
>
And in fact this is probably a better way to combine several 'signals'
in one plot to be honest.
> > Third, I have created densityplots and noticed that the order of files
> > is not like the order in the phenoData info. In phenoData the files are
> > ordered according to their file-names (or more precise by the trailing
> > numbers given by CellQuest), while they are plotted in some kind of
> > alphabetical order in densityplot. Is it possible to pass an argument to
> > densityplot that will plot the files in the file-names order?
>
> Yes, that's the default for factor levels (see ?factor) when the file
> names get converted to a factor. You can control the order by
> specifying the levels explicitly. For example, compare:
>
> densityplot(factor(name, levels = rev(unique(name))) ~`FL1-H`, data =
> fs.trans[1:5])
>
> and
>
> densityplot(factor(name, levels = unique(name)) ~`FL1-H`, data = fs.trans[1:5])
>
Exactly what I needed! Perfect.
> > And is it also possible to have the plot in black and white and not in color?
>
> Yes, e.g.
>
> densityplot( ~`FL1-H`, data = fs.trans[1:5], par.settings =
> standard.theme(color = FALSE))
>
> See ?trellis.device and ?flowViz.par.get for more details.
>
I admit that the higher plot functions are still a bit of a miracle to
me but I think I start getting how to change some higher level
functions.
> > I have also tried different gates and managed to create ellipsoid,
> > rectangular and n2Filter, but failed to produce a polygon gate. Could
> > anyone provide me with an simple example how to do that?
>
> See the example in ?polygonGate.
>
Ok, I missed this example, my fault. I have now managed to get an
polygon gate!
> > And a last question, how could I produce a densityplot where I have an
> > overaly instead of shingles for several files in one figure (such as is
> > often used for publications, to show the shift from unstained, isotype
> > control to specific staining).
>
> Unfortunately that's not yet supported by the "flowSet" densityplot
> method. You could however use the underlying lattice functions
> directly to get what you want:
>
> tmpe <-
> fsApply(fs.trans[1:6],
> function(x) exprs(x)[, "FL1-H"],
> simplify = FALSE)
>
> densityplot(~data, do.call(make.groups, tmpe), groups = which,
> plot.points = FALSE, auto.key = list(columns = 3))
>
This works nicely too. Thanks.
> -Deepayan
I have another question now. I was wondering if I can use four
rectangular gates at the same time. This would be a bit like having
quadrant statistics in other FACS software. I tried this by creating
four gates with
UL <- rectangleGate(filterId='UL', 'SSC-H' = c(400, 1000), 'FSC-H' =
c(0,500))
LL <- rectangleGate(filterId='LL', 'SSC-H' = c(0, 400), 'FSC-H' =
c(0,500))
UR <- rectangleGate(filterId='UR', 'SSC-H' = c(400, 1000), 'FSC-H' =
c(500,1000))
LR <- rectangleGate(filterId='LR', 'SSC-H' = c(0, 400), 'FSC-H' =
c(500,1000))
Now I can create subsets for each of these gates and get the percentages
gated and create results with
result_LL <- filter(fs.trans[1:4], LL)
Percent.LL <- lapply(result_LL, summary)
Percent.LL
I have used FSC and SSC for this example but obviously this is something
I eventually want to do with two fluorescent channels to identify double
positive populations.
I was wondering if I can now create a graph in which all 4 gates are
plotted and the percentage in each gate is also plotted?
I have failed in plotting all 4 gates and I looked at the filterSet
function but I am not sure if making a filter set is the right way to do
this? And in fact I am not sure that this is possible at all. But from
what I have figured out about lattice I thought that it is possible to
'add' further information to a graph after it is created. Maybe you can
point me in the right direction how to do this?
And I would like to thank you for the time and effort you have put into
making this package for Flow-data. I have been searching for
Flow-software working in Linux some time now and really this is the
first time I have come across something that allows me to get some nice
output and at the same time control over what I am doing with my data. I
have used R mainly for microarray data in the past, so my learning curve
wasn't that steep this time, so this might not be true for first time
users. But I can only recommend taking the time to learn how to use
flowViz to anyone looking for Linux based Flow-software.
Thanxs,
Anja
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