plot.gene() with smaller key color steps?
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Paul Hammer ▴ 220
@paul-hammer-2635
Last seen 9.7 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
affy affy • 592 views
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