dna_seg {genoPlotR}

DNA segment (dna_seg) class and class functions

Description

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.

Usage

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)

Arguments

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.

Details

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.

Value

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.

Author(s)

Lionel Guy

See Also

read_dna_seg_from_tab, read_dna_seg_from_ptt, gene_types.

Examples

## 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)