Entering edit mode
Aric Gregson
▴
270
@aric-gregson-3058
Last seen 10.2 years ago
Hello,
I don't believe that I have seen an explanation and I suspect that I
am
not calling the filter appropriately. Using flowStats in a workFlow
with a quadrantGate making a filter I can easily plot the results with
the xyplot if smooth=TRUE (the default). However, when the populations
get small smooth=T is inadequate to visualize the results. Setting
smooth=F results in:
error in evaluating the argument 'subset' in selecting a method for
'Subset'
quad <- quadrantGate(Data(wf[["CD4+CD3+"]]),
stains=c("Pacific.Blue.A","Alexa.Fluor.700.A"),
plot=TRUE,
filterId="quad",
borderQuant=0.3,
alpha=c(1,1),
sd=c(0.6,0.6),
refLine.1=5,
refLine.2=5)
add(wf, quad, parent="CD4+CD3+")
-> This works fine:
xyplot(`Alexa.Fluor.700.A` ~ `Pacific.Blue.A` | Filename,
Data(wf[['CD4+CD3+']]),
filter=quad)
-> This fails with the above error message:
xyplot(`Alexa.Fluor.700.A` ~ `Pacific.Blue.A` | Filename,
Data(wf[['CD4+CD3+']]),
smooth=F,
filter=quad) -> I have tried to access gate, boundX/Y but not able
This is consistent and can be replicated with the GvHD set using a
similar filter setup.
Thanks in advance.
Aric
sessionInfo()
R version 2.11.0 (2010-04-22)
amd64-portbld-freebsd8.1
locale:
[1] C
attached base packages:
[1] grid tools splines stats graphics grDevices
utils [8] datasets methods base
other attached packages:
[1] Rgraphviz_1.26.0 graph_1.26.0 flowQ_1.9.0
[4] latticeExtra_0.6-11 RColorBrewer_1.0-2 parody_1.6.0
[7] bioDist_1.20.0 KernSmooth_2.23-3 outliers_0.13-2
[10] flowStats_1.7.5 cluster_1.12.3 mvoutlier_1.4
[13] fda_2.2.2 zoo_1.6-4 flowViz_1.13.1
[16] lattice_0.18-5 flowCore_1.15.2 rrcov_1.0-01
[19] pcaPP_1.8-2 mvtnorm_0.9-92 robustbase_0.5-0-1
[22] Biobase_2.8.0 fortunes_1.3-7
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.10.2 DBI_0.2-5 MASS_7.3-5
[4] RSQLite_0.9-2 annotate_1.26.1 feature_1.2.4
[7] geneplotter_1.26.0 ks_1.6.13 stats4_2.11.0
[10] xtable_1.5-6