# seg_plot class and class functions An seg_plot is an object to plot data associated to a `dna_seg` object. It is a `list` with mandatory and optional arguments. The main arguments are `func`, which is a function returning a `grob` or a `gList`, and `args`, which are arguments to be passed to this function. ```r seg_plot(func, args = NULL, xargs = c("x", "x0", "x1", "x2", "v"), yargs = c("y", "y0", "y1", "y2", "h"), ylim = NULL) as.seg_plot(seg_plot) is.seg_plot(seg_plot) ``` ## Arguments - `func`: Mandatory, with no defaults. A function that returns a `grob` object. See `grid` documentation to find ready-made functions. User-defined functions work too. - `args`: A list, `NULL` by default. The arguments that will be passed to the function. It is recommended that all arguments are named. - `xargs`: A vector giving the names of which of the arguments in `args` are defining the x-axis. Used, among others, by the function `trim.seg_plot`. By default, gives the most common x-defining arguments of the `grid` functions (x, x0, x1, x2, v). - `yargs`: A vector giving the names of which of the arguments in `args` are defining the y-axis. Used when plotting the graphs to define a sensible `ylim` if not defined. By default, gives the most common y-defining arguments of the `grid` functions (y, y0, y1, y2, h). - `ylim`: A numeric vector of length 2, defining the range of the plot when drawn with `plot_gene_map`. Derived from `yargs` if not set. - `seg_plot`: In `as.seg_plot`, a `list` object to convert to `seg_plot`. See details below. In `is.seg_plot`, an object to test. ## Returns `seg_plot` and `as.seg_plot` return a `seg_plot` object. `is.seg_plot` returns a logical. ## Details A `seg_plot` object is an object describing how to plot data associated to a `dna_seg`. It is a list composed of a function, arguments to pass to this function, two arguments to define which of those define x and y, and an eventual `ylim` to limit the plotting to a certain range when plotting. The function `func` should return a `grob` object, or a `gList` list of `grob`s. The predefined functions of `grid`, such as `linesGrob`, `pointsGrob`, `segmentsGrob`, `textGrob` or `polygonGrob` can be used, or user-defined functions can be defined. The arguments in `args` should correspond to arguments passed to `func`. For example, if `func = pointsGrob`, `args` could contain the elements `x = 10:1`, `y = 1:10`. It will often also contain a `gp` element, the result of a call to the `gpar` function, to control graphical aspects of the plot such as color, fill, line width and style, fonts, etc. ## Author(s) Lionel Guy ## See Also `plot_gene_map`, `trim.seg_plot`. ## Examples ```r ## Using the existing pointsGrob 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))) is.seg_plot(sp) ## Function seg_plot(...) is identical to as.seg_plot(list(...)) sp2 <- as.seg_plot(list(func=pointsGrob, args=list(x=x, y=y, gp=gpar(col=1:20, cex=1:3)))) identical(sp, sp2) ## For the show, plot the obtained result grb <- do.call(sp$func, sp$args) ## Trim the seg_plot sp_trim <- trim(sp, c(3, 10)) ## Changing color and function "on the fly" sp_trim$args$gp$col <- "blue" sp_trim$func <- linesGrob grb_trim <- do.call(sp_trim$func, sp_trim$args) ## Now plot plot.new() pushViewport(viewport(xscale=c(0,21), yscale=c(-4,4))) grid.draw(grb) grid.draw(grb_trim) ## Using home-made function triangleGrob <- function(start, end, strand, col, ...) { x <- c(start, (start+end)/2, end) y1 <- 0.5 + 0.4*strand y <- c(y1, rep(0.5, length(y1)), y1) polygonGrob(x, y, gp=gpar(col=col), default.units="native", id=rep(1:7, 3)) } start <- seq(1, 19, by=3)+rnorm(7)/3 end <- start + 1 + rnorm(7) strand <- sign(rnorm(7)) sp_tr <- seg_plot(func=triangleGrob, args=list(start=start, end=end, strand=strand, col=1:length(start)), xargs=c("start", "end")) grb_tr <- do.call(sp_tr$func, sp_tr$args) plot.new() pushViewport(viewport(xscale=c(1,22), yscale=c(-2,2))) grid.draw(grb_tr) ## Trim sp_tr_trim <- trim(sp_tr, xlim=c(5, 15)) str(sp_tr_trim) ## If the correct xargs are not indicated, trimming won't work sp_tr$xargs <- c("x") sp_tr_trim2 <- trim(sp_tr, xlim=c(5, 15)) identical(sp_tr_trim, sp_tr_trim2) y1 <- convertY(grobY(grb_tr, "south"), "native") y2 <- convertY(grobY(grb_tr, "north"), "native") heightDetails(grb) grb ## Applying it to plot_gene_maps data(three_genes) ## Build data to plot xs <- lapply(dna_segs, range) colors <- c("red", "blue", "green") seg_plots <- list() for (i in 1:length(xs)){ x <- seq(xs[[i]][1], xs[[i]][2], length=20) seg_plots[[i]] <- seg_plot(func=pointsGrob, args=list(x=x, y=rnorm(20)+2*i, default.units="native", pch=3, gp=gpar(col=colors[i], cex=0.5))) } plot_gene_map(dna_segs, comparisons, seg_plots=seg_plots, seg_plot_height=0.5, seg_plot_height_unit="inches", dna_seg_scale=TRUE) ## A more complicated example data(barto) tree <- newick2phylog("(BB:2.5,(BG:1.8,(BH:1,BQ:0.8):1.9):3);") ## Showing several subsegments per genome xlims2 <- list(c(1445000, 1415000, 1380000, 1412000), c( 10000, 45000, 50000, 83000, 90000, 120000), c( 15000, 36000, 90000, 120000, 74000, 98000), c( 5000, 82000)) ## Adding fake data in 1kb windows seg_plots <- lapply(barto$dna_segs, function(ds){ x <- seq(1, range(ds)[2], by=1000) y <- jitter(seq(100, 300, length=length(x)), amount=50) seg_plot(func=linesGrob, args=list(x=x, y=y, gp=gpar(col=grey(0.3), lty=2))) }) plot_gene_map(barto$dna_segs, barto$comparisons, tree=tree, seg_plots=seg_plots, seg_plot_height=0.5, seg_plot_height_unit="inches", xlims=xlims2, limit_to_longest_dna_seg=FALSE, dna_seg_scale=TRUE, main="Random plots for the same segment in 4 Bartonella genomes") ```

seg_plot function