dna_seg {genoPlotR} | R Documentation |
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 |
... |
Arguments further passed to |
df |
A data frame representing the |
col |
Either a color vector of the same length as |
fill |
Either a fill vector of the same length as |
lty |
A vector of the same length as |
lwd |
Same as |
pch |
Same as |
cex |
Same as |
gene_type |
Vector of the same length as |
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)