Commit ⋅ darunabas/phyloregion

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@@ -15,9 +15,11 @@

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#' @rdname plot_structure
#' @importFrom graphics Axis barplot layout
#' @importFrom utils modifyList
#' @importFrom sp coordinates<- CRS proj4string<- SpatialPolygonsDataFrame
#' @importFrom sp coordinates<- over CRS proj4string merge
#' @return Returns no value, just visualize structure plot!
#' @export
plot_structure <- function(omega, shp, by = NULL, col=hcl.colors(12), ...) {
plot_structure <- function(omega, shp, by = NULL, col=hcl.colors(15), ...) {

    #shp <- obj$shp
    #omega <- obj$omega

@@ -26,10 +28,29 @@

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    s1 <- subset(shp, shp$grids %in% index)

    if (!is.null(by)) {
        s1 <- s1[, c("grids", by)]
        names(s1) <- c("grids", "by")
        sx <- split(s1, f=s1$by)
        vv <- as.numeric(matrix(lapply(sx, function(x) nrow(x)/nrow(s1))))
        if (inherits(by, "SpatialPolygonsDataFrame")) {
            w <- s1[, "grids"]
            suppressWarnings(proj4string(by) <- proj4string(w))
            r <- suppressWarnings(cbind(as.data.frame(w), sp::over(w, by)))
            d <- merge(w, r, by="grids")
            d <- d[, c(1, 2)]
            names(d) <- c("grids", "by")
            d <- d[!is.na(d@data$by),]
        } else {
            d <- s1[, c("grids", by)]
            names(d) <- c("grids", "by")
        }

        tmp <- names(which(table(d$by)<2))
        if(length(tmp)>0) {
            print("Dropping sites because they have only one grid cell:")
            print(tmp)
        }

        d <- subset(d, !(d$by %in% tmp))

        sx <- split(d, f=d$by)
        vv <- as.numeric(matrix(lapply(sx, function(x) nrow(x)/nrow(d))))

        nf <- layout(matrix(1:length(sx), ncol=1), heights=vv)


@@ -40,10 +61,9 @@

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            par(mgp=c(3,0,0))
            par(mar=c(0, 5, 0, 1))
            barplot(z1, horiz=TRUE, col=col,
                    border=NA, space=0, las=1,
                    axes=FALSE, ylab=x$by[1], cex.lab=0.75)

        })))
                    border = if (nrow(d) < 200) "black" else NA,
                    space=0, las=1,
                    axes=FALSE, ylab=x$by[1], cex.lab=0.75)})))
    } else {
        ind1 <- intersect(s1$grids, row.names(omega))
        y1 <- omega[ind1,]

Files		•	•	•	Coverage
R	1,462	114	0	1,348	7.80%
Project Totals (37 files)	1,462	114	0	1,348	7.80%

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15	15		#' @rdname plot_structure
16	16		#' @importFrom graphics Axis barplot layout
17	17		#' @importFrom utils modifyList
	18	+	#' @importFrom sp coordinates<- CRS proj4string<- SpatialPolygonsDataFrame
	19	+	#' @importFrom sp coordinates<- over CRS proj4string merge
18	20		#' @return Returns no value, just visualize structure plot!
19	21		#' @export
20		-	plot_structure <- function(omega, shp, by = NULL, col=hcl.colors(12), ...) {
	22	+	plot_structure <- function(omega, shp, by = NULL, col=hcl.colors(15), ...) {
21	23
22	24		#shp <- obj$shp
23	25		#omega <- obj$omega

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26	28		s1 <- subset(shp, shp$grids %in% index)
27	29
28	30		if (!is.null(by)) {
29		-	s1 <- s1[, c("grids", by)]
30		-	names(s1) <- c("grids", "by")
31		-	sx <- split(s1, f=s1$by)
32		-	vv <- as.numeric(matrix(lapply(sx, function(x) nrow(x)/nrow(s1))))
	31	+	if (inherits(by, "SpatialPolygonsDataFrame")) {
	32	+	w <- s1[, "grids"]
	33	+	suppressWarnings(proj4string(by) <- proj4string(w))
	34	+	r <- suppressWarnings(cbind(as.data.frame(w), sp::over(w, by)))
	35	+	d <- merge(w, r, by="grids")
	36	+	d <- d[, c(1, 2)]
	37	+	names(d) <- c("grids", "by")
	38	+	d <- d[!is.na(d@data$by),]
	39	+	} else {
	40	+	d <- s1[, c("grids", by)]
	41	+	names(d) <- c("grids", "by")
	42	+	}
	43	+
	44	+	tmp <- names(which(table(d$by)<2))
	45	+	if(length(tmp)>0) {
	46	+	print("Dropping sites because they have only one grid cell:")
	47	+	print(tmp)
	48	+	}
	49	+
	50	+	d <- subset(d, !(d$by %in% tmp))
	51	+
	52	+	sx <- split(d, f=d$by)
	53	+	vv <- as.numeric(matrix(lapply(sx, function(x) nrow(x)/nrow(d))))
33	54
34	55		nf <- layout(matrix(1:length(sx), ncol=1), heights=vv)
35	56

40	61		par(mgp=c(3,0,0))
41	62		par(mar=c(0, 5, 0, 1))
42	63		barplot(z1, horiz=TRUE, col=col,
43		-	border=NA, space=0, las=1,
44		-	axes=FALSE, ylab=x$by[1], cex.lab=0.75)
45		-
46		-	})))
	64	+	border = if (nrow(d) < 200) "black" else NA,
	65	+	space=0, las=1,
	66	+	axes=FALSE, ylab=x$by[1], cex.lab=0.75)})))
47	67		} else {
48	68		ind1 <- intersect(s1$grids, row.names(omega))
49	69		y1 <- omega[ind1,]