genoPlotR (version 0.8.11)

trim: Trimming data frames or more complex objects with >= 2 numeric columns

Description

Trims data frames with 2 or more numeric columns using a xlim. xlim(s) are as used to filter rows whose numeric values are included in this interval.

Usage

trim(x, ...)
# S3 method for default
trim(x, xlim = NULL, ...)
# S3 method for dna_seg
trim(x, xlim = NULL, ...)
# S3 method for comparison
trim(x, xlim1 = c(-Inf, Inf), xlim2 = c(-Inf, Inf), ...)
# S3 method for annotation
trim(x, xlim = NULL, ...)
# S3 method for seg_plot
trim(x, xlim = NULL, ...)

Arguments

x

An object to trim,. generally a data frame or a matrix, or a seg_plot object.

xlim

A numeric of length 2. In a general case, the rows whose values are included in this interval are returned.

…

Unused.

xlim1

A numeric of length 2. In the case of comparison, where the comparison can be filtered on two sides, the interval to filter the first side.

xlim2

A numeric of length 2. The interval to filter the second side.

Value

Returns the same object as input, with the rows (or subset) corresponding to the given interval.

Details

In the case where x is a seg_plot object, the function uses the xargs argument to define what are the vectors defining the x position (they should be the same length). Then, all the arguments (including those inside an eventual gp argument) that are the same length as the x vectors are trimmed, so that only the rows for which the x values are inside the xlim argument are kept.

See Also

dna_seg, comparison, seg_plot.

Examples

# NOT RUN {
## Load
data(barto)
xlim_ref <- c(10000, 45000)
## Seg 2 (ref)
barto$dna_segs[[2]] <- trim(barto$dna_segs[[2]], xlim=xlim_ref)
## Seg 1
barto$comparisons[[1]] <- trim(barto$comparisons[[1]], xlim2=xlim_ref)
xlim1 <- range(barto$comparisons[[1]], overall=FALSE)$xlim1
barto$dna_segs[[1]] <- trim(barto$dna_segs[[1]], xlim=xlim1)
## Seg 3
barto$comparisons[[2]] <- trim(barto$comparisons[[2]], xlim1=xlim_ref)
xlim3 <- range(barto$comparisons[[2]], overall=FALSE)$xlim2
barto$dna_segs[[3]] <- trim(barto$dna_segs[[3]], xlim=xlim3)
## Seg 4
barto$comparisons[[3]] <- trim(barto$comparisons[[3]], xlim1=xlim3)
xlim4 <- range(barto$comparisons[[3]], overall=FALSE)$xlim2
barto$dna_segs[[4]] <- trim(barto$dna_segs[[4]], xlim=xlim4)
## Plot
plot_gene_map(barto$dna_segs, barto$comparisons)

## With seg_plot
x <- 1:20
y <- rnorm(20)
sp <- seg_plot(func=pointsGrob, args=list(x=x, y=y,
                                  gp=gpar(col=1:20, cex=1:3)))
## Trim 
sp_trim <- trim(sp, c(3, 10))
str(sp_trim)
range(sp_trim$arg$x)
# }