Question: interactions of range(flowFrame) with transform, densityplot and splom

0

Mroz, Edmund A. •

**10**wrote:
In using the flowCore and flowViz packages, I came up against two
problems,
apparently related to how transform() re-sets ranges, and how
densityplot() and
splom() get their limits from range().
I was wondering if I was doing something wrong, if these are necessary
features,
or are inadvertent glitches. I haven't seen them mentioned in the
archives.
They can be seen with a subset (Time,SSC-H,FL2-A) of a flowFrame from
the GvHD
data.
> library(flowViz)
> data(GvHD)
> f1<-GvHD[[1]][,c(8,2,6)]
Problem 1: transform() and range(), with densityplot()
Create two derived columns with transform():
> f1<-transform(f1,sumCol=`SSC-H`+`FL2-A`,diffCol=`SSC-H`-`FL2-A`)
splom shows a wide range of all data
> splom(f1)
but densityplot() gives a trivial plot for diffCol, not representative
of the
data. Compare:
> densityplot(~.,f1)
> hist(exprs(f1)[,"diffCol"])
This might arise from densityplot() taking limits from the range of
the
flowFrame, which gave the following after transform():
> range(f1)
?Time SSC-H FL2-A sumCol diffCol
min ???0 ????0 ????0 ?????0 ??????0
max 1023 ?1023 ?1023 ??2046 ??????0
The values for range(f1) in the added columns seem to have been
obtained by
arithmetic on the ranges of the source columns, rather than obtained
from ranges
after transformation.
I understand that is the desired result for single-column data
transformations,
but this poses a problem for on-the-fly plotting of transformations
involving
multiple columns of flowFrames and flowSets. (I originally found it
when taking
the difference of 2 log-transformed columns, to get the log of their
ratio.)
-------------------
Problem 2: splom() and plotting range
I found this problem when my data had Time as the first data column,
with a wide
time range. To illustrate, simply change the "maxRange" for Time in
the above
example:
> pData(parameters(f1))[1,"maxRange"]<-10000
> range(f1)
??Time SSC-H FL2-A sumCol diffCol
min ????0 ????0 ????0 ?????0 ??????0
max 10000 ?1023 ?1023 ??2046 ??????0
Now, with:
> splom(f1)
the limits on the SSC-H axes (and for density calculation) seem to
have been
taken from the first data column (Time),?not from the SSC-H column,
constricting
the output and leading to error messages from KernSmooth::bkde2D().
My initial look at the code for splom(flowFrame) suggests that scales
for splom
are obtained from all data columns, even when exclude.time=TRUE,
although I
might be misinterpreting the code.
If my interpretation is correct, this poses a problem for splom() if
Time isn't
the last column and exclude.time=TRUE.
My sessionInfo() follows. Thanks for your help.
Ed Mroz
Surgical Oncology Research
MGH Cancer Center
Boston, MA
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats ????graphics ?grDevices utils ????datasets ?methods ??base
other attached packages:
[1] flowViz_1.14.0 ????lattice_0.19-13 ???flowCore_1.16.0
[4] rrcov_1.1-00 ??????pcaPP_1.8-3 ???????mvtnorm_0.9-92
[7] robustbase_0.5-0-1 Biobase_2.10.0
loaded via a namespace (and not attached):
[1] feature_1.2.5 ??????graph_1.28.0 ???????grid_2.12.0
[4] KernSmooth_2.23-4 ??ks_1.7.4 ???????????latticeExtra_0.6-14
[7] MASS_7.3-8 ?????????RColorBrewer_1.0-2 ?stats4_2.12.0
[10] tools_2.12.0
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