genoPlotR (version 0.7)

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

## 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)