genoPlotR-package: genoPlotR - a R framework to produce publication-grade maps...

Description Details Author(s) See Also Examples

Description

A R framework to plot comparison of gene stretches or genomes, a la ACT (Artemis Comparison Tool), but with production-grade graphics, and a static interface. Reads directly from tabular files or from wide-spread biological formats such as BLAST and PTT (NCBI).

Details

Package: genoPlotR
Type: Package
Version: 0.1
Date: 2009-12-08
License: GPL (>=2)
LazyLoad: yes

The only plotting function is plot_gene_map, which produces link[grid]{grid} graphics. Data is composed mainly of DNA segments (dna_seg) objects, which represent collections of genes or segments of genomes, and of comparison objects, which are the pairwise comparisons between the dna_segs. Data can be read from files (see read_functions) or from R objects like data.frames or lists, with dna_seg and comparison conversion functions.

Author(s)

Lionel Guy

Maintainer: Lionel Guy [email protected]

See Also

plot_gene_map for plotting. dna_seg and comparison for the base objects and conversion functions. read_dna_seg_from_tab, read_dna_seg_from_ptt, read_comparison_from_tab and read_comparison_from_blast to read from files.

Examples

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## simple example
## dna segments
## data.frame with several genes
names1 <- c("feat1", "feat2", "feat3")
starts1 <- c(2, 1000, 1050)
ends1 <- c(600, 800, 1345)
strands1 <- c("-", -1, 1)
cols1 <- c("blue", "grey", "red")
df1 <- data.frame(name=names1, start=starts1, end=ends1,
                  strand=strands1, col=cols1)
dna_seg1 <- dna_seg(df1)
is.dna_seg(dna_seg1)

## with only one gene, or two, and merging
gene2a <- dna_seg(list(name="feat1", start=50, end=900, strand="-", col="blue"))
genes2b <- dna_seg(data.frame(name=c("feat2", "feat3"), start=c(800, 1200),
                              end=c(1100, 1322), strand=c("+", 1),
                              col=c("grey", "red")))
dna_seg2 <- c.dna_seg(gene2a, genes2b)
is.dna_seg(dna_seg2)

## reading from file
dna_seg3_file <- system.file('extdata/dna_seg3.tab', package = 'genoPlotR')
dna_seg3 <- read_dna_seg_from_tab(dna_seg3_file)
is.dna_seg(dna_seg3)

## comparison
## from a data.frame
comparison1 <- as.comparison(data.frame(start1=starts1, end1=ends1,
                                        start2=dna_seg2$start,
                                        end2=dna_seg2$end))
is.comparison(comparison1)

## from a file
comparison2_file <- system.file('extdata/comparison2.tab',
                                package = 'genoPlotR')
comparison2 <- read_comparison_from_tab(comparison2_file,
                                        color_scheme="red_blue")
is.comparison(comparison1)

## plot
plot_gene_map(dna_segs=list(dna_seg1, dna_seg2, dna_seg3),
              comparisons=list(comparison1, comparison2)) 

genoPlotR documentation built on Sept. 13, 2017, 3:01 p.m.