dna_seg: DNA segment (dna_seg) class and class functions
In genoPlotR: Plot Publication-Grade Gene and Genome Maps

Description Usage Arguments Details Value Author(s) See Also Examples

A DNA segment is a collection of genes or elements along a genome, to be represented on a map. These functions are class functions to create, convert and test dna_seg objects.

dna_seg(x, ...)
as.dna_seg(df, col = "blue", fill = "blue", lty = 1, lwd = 1,
           pch = 8, cex = 1, gene_type = "arrows")
is.dna_seg(dna_seg)

`x`	A `data.frame` or `list` that can be coerced to a data frame.
`...`	Arguments further passed to `as.dna_seg` (see below).
`df`	A data frame representing the `dna_seg` object. See details for necessary columns.
`col`	Either a color vector of the same length as `df` or of length one, to be applied to the whole object. Will be passed to corresponding `grob` object. Default to blue.
`fill`	Either a fill vector of the same length as `df` or of length one, to be applied to the whole object. Will be passed to corresponding `grob` object. Default to `blue`.
`lty`	A vector of the same length as `df` or of length one, giving the line type around the objects.
`lwd`	Same as `lty`, giving the line width.
`pch`	Same as `lty`, giving the character representing each object. Goes with `gene_type` points.
`cex`	Same as `lty`, giving the character size representing each object. Goes with `gene_type` points.
`gene_type`	Vector of the same length as `df` or of length one, giving the type of representation of each object.
`dna_seg`	Object to test.

Objects to be converted needs to have their first 4 columns named name, start, end and strand. Extra columns with names col, lty, lwd, pch, cex, gene_type will be used in the plotting process. Other extra columns will be kept in the object, but not used.

dna_seg tries to build a dna_seg object from a data frame or a list.

as.dna_seg tries to build a dna_seg object from a data frame.

Read functions such as read_dna_seg_from_tab and read_dna_seg_from_ptt also return dna_seg objects.

A comparison object for comparison and as.comparison. DNA seg objects are also of class data.frame. They contain the following columns: name, start, end, strand, col, lty, lwd, pch, cex, gene_type.

A logical for is.comparison.

Lionel Guy

read_dna_seg_from_tab, read_dna_seg_from_ptt, gene_types.

## generate data
names1 <- c("feat1", "feat2", "feat3")
starts1 <- c(2, 1000, 1050)
ends1 <- c(600, 800, 1345)
strands1 <- c("-", -1, 1)
cols1 <- c("blue", "grey", "red")

## create data.frame
df1 <- data.frame(name=names1, start=starts1, end=ends1,
                  strand=strands1, col=cols1)

## with dna_seg
dna_seg1 <- dna_seg(df1)
dna_seg1
as.dna_seg(df1)

## test
is.dna_seg(dna_seg1)

## directly readable with read_dna_seg_from_tab
## Not run: 
write.table(x=dna_seg1, file="dna_seg1.tab", quote=FALSE,
            row.names=FALSE, sep="\t")

## End(Not run)

## with only one gene and with list, or two, and merging with c.dna_seg
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"),
                              fill=c("transparent", "grey"),
                              gene_type=c("arrows", "blocks")))
dna_seg2 <- c(gene2a, genes2b)

## test
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)