genoPlotR-package: Plot Publication-Grade Gene and Genome Maps

In genoPlotR: Plot Publication-Grade Gene and Genome Maps

Description

Draws gene or genome maps and comparisons between these, in a publication-grade manner. Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.

Details

This package was not yet installed at build time.

Index: This package was not yet installed at build time.
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 <[e-mail]>

Maintainer: Lionel Guy <[e-mail]>

References

Guy, L., Roat Kultima, J, and Andersson, S.G.E. (2010). genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26(18):2334-2335.

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

## 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)) 

Example output

Loading required package: ade4
Loading required package: grid
[1] TRUE
[1] TRUE
[1] TRUE
[1] TRUE
[1] TRUE

genoPlotR documentation built on Jan. 7, 2021, 5:08 p.m.