Hi,

Hope you're fine…
I am trying to make whole genome plots using the geneplotter
package/annotate package. The organism I am studying is Arabidopsis
thaliana, and obviously the annotations are not so extensive there: when
trying to build a chromLocation object, I can't obviously do that (see error
below)
It is obvious to me, that the chromosome location mappings are not provided
in the Arabidopsis anntation package (see below).

My question: is there any way of plotting Arabidopsis gene expression data
along a chromosome. Should I just order the GeneIds (luckily, for the TAIR
Ids one can infer the gene order along a chromosome)? Has anyone made a
script for this?

Thanks for any help, best wishes,

Sam


> library(ath1121501.db)
> newChrClass <- buildChromLocation("ath1121501")
Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
  variable "ath1121501CHRLENGTHS" was not found

> objects("package:ath1121501.db")
 [1] "ath1121501"             "ath1121501ACCNUM"
"ath1121501ARACYC"       "ath1121501ARACYCENZYME" "ath1121501CHR"
 [6] "ath1121501CHRLOC"       "ath1121501ENZYME"
"ath1121501ENZYME2PROBE" "ath1121501GENENAME"     "ath1121501GO"
[11] "ath1121501GO2ALLPROBES" "ath1121501GO2PROBE"
"ath1121501MAPCOUNTS"    "ath1121501MULTIHIT"     "ath1121501ORGANISM"
[16] "ath1121501PATH"         "ath1121501PATH2PROBE"
"ath1121501PMID"         "ath1121501PMID2PROBE"   "ath1121501SYMBOL"
[21] "ath1121501_dbInfo"      "ath1121501_dbconn"
"ath1121501_dbfile"      "ath1121501_dbschema"

> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-apple-darwin8.10.1

locale:
en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
 [1] ath1121501.db_2.2.0  TinesATH1.db_1.0     geneplotter_1.18.0
annotate_1.18.0      xtable_1.5-2         AnnotationDbi_1.2.0

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