Entering edit mode
Paul Hammer
▴
220
@paul-hammer-2635
Last seen 10.3 years ago
hi members,
i try to plot genes with the function plot.gene(). Actually it works
fine but i would like to change the key color value steps. now i have
a
range from 0 till 12 with 1 per step (12 different colors). Because
the
expression values are in log scale it would be better to separate the
color steps to 0.1 (120 colors).
here my R code:
plot.gene("gene", affy.rma, gps=list(22:24), type="mean-int",
col.range=c(0,12), use.symbol=TRUE, use.mt=FALSE, probes.min = 4,
main="
Intensity", border.col="black", text.col="black", text.bg="white",
exon.borders=FALSE, show.legend=TRUE)
any suggestions?
thanks
paul
> sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.
UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8
;LC_IDENTIFICATION=C
attached base packages:
[1] splines tools stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] gplots_2.3.2 gdata_2.4.0 gtools_2.4.0
[4] exonmap_1.4.3 plier_1.8.0 RMySQL_0.6-0
[7] DBI_0.2-4 RColorBrewer_1.0-2 simpleaffy_2.14.05
[10] gcrma_2.10.0 matchprobes_1.10.0 genefilter_1.16.0
[13] survival_2.34 affy_1.16.0 preprocessCore_1.0.0
[16] affyio_1.6.1 Biobase_1.16.3
loaded via a namespace (and not attached):
[1] annotate_1.16.1 AnnotationDbi_1.0.6 rcompgen_0.1-17
[4] RSQLite_0.6-8