Created
December 14, 2024 12:57
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simple subregion select and crop
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| library(SpatialData) | |
| library(SpatialData.data) | |
| library(sf) | |
| library(ggplot2) | |
| if (!exists("br")) br = Breast2fov_10x() | |
| brsh = shape(br) | |
| library(SpatialData.plot) | |
| # some points to form a subregion | |
| pick = structure(list(x = c(355.185319678255, 353.624236083554, 510.140679646861, | |
| 496.285253053229, 355.185319678255), y = c(-471.421489018199, | |
| -591.83220661942, -601.010859954238, -467.21109758021, -471.421489018199 | |
| )), row.names = c(NA, -5L), class = "data.frame") | |
| plotSpatialData() + plotShape(br, c="black") + geom_path(data=pick, aes(x=x,y=abs(y), colour="red")) # full dataset | |
| pick_poly = st_polygon(list(abs(data.matrix(pick)))) | |
| brshpoly = st_as_sf(brsh@data) | |
| trim = st_intersects(brshpoly, pick_poly, sparse=FALSE) | |
| sh251 = brshpoly[i=which(trim[,1]),] | |
| par(ask=TRUE) | |
| picked = ShapeFrame(as.data.frame(sh251)) | |
| if (!("pick" %in% shapeNames(br))) shapes(br)$pick = picked | |
| plotSpatialData() + plotShape(br, "pick", c="black") |
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