tests/testthat/test_plotSpatial.R
In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis
test_that("plotSpatial function works", {
library(cytomapper)
library(ggraph)
data("pancreasSCE")
cur_sce1 <- pancreasSCE[,pancreasSCE$ImageNb == 1]
cur_sce2 <- pancreasSCE[,pancreasSCE$ImageNb == 2]
cur_sce3 <- pancreasSCE[,pancreasSCE$ImageNb == 3]
cur_sce1$Pos_X <- cur_sce1$Pos_X - min(cur_sce1$Pos_X)
cur_sce1$Pos_Y <- cur_sce1$Pos_Y - min(cur_sce1$Pos_Y)
cur_sce2$Pos_X <- cur_sce2$Pos_X - min(cur_sce2$Pos_X)
cur_sce2$Pos_Y <- cur_sce2$Pos_Y - min(cur_sce2$Pos_Y)
cur_sce3$Pos_X <- cur_sce3$Pos_X - min(cur_sce3$Pos_X)
cur_sce3$Pos_Y <- cur_sce3$Pos_Y - min(cur_sce3$Pos_Y)
pancreasSCE <- cbind(cur_sce1, cur_sce2, cur_sce3)
cur_sce <- pancreasSCE
# SingleCellExperiment
expect_silent(p <- plotSpatial(cur_sce, img_id = "ImageNb"))
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$CellType, pancreasSCE$CellType)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Area, pancreasSCE$Area)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "Pattern")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Pattern, pancreasSCE$Pattern)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN", assay_type = "counts")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$PIN, counts(pancreasSCE)["PIN",], check.attributes = FALSE)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN", assay_type = "exprs")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$PIN, assay(pancreasSCE, "exprs")["PIN",], check.attributes = FALSE)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CDH", assay_type = "exprs")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$CDH, assay(pancreasSCE, "exprs")["CDH",], check.attributes = FALSE)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$CellType, pancreasSCE$CellType)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = "Area")
expect_s3_class(p, "ggraph")
expect_warning(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Area, as.character(pancreasSCE$Area))
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = "Pattern")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Pattern, as.character(pancreasSCE$Pattern))
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = "CellType")
expect_s3_class(p, "ggraph")
#expect_warning(print(p), regexp = "Using size for a discrete variable is not advised.")
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$CellType, pancreasSCE$CellType)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Area, pancreasSCE$Area)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = "Pattern")
expect_s3_class(p, "ggraph")
#expect_warning(print(p), regexp = "Using size for a discrete variable is not advised.")
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Pattern, pancreasSCE$Pattern)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType",
node_shape_by = "Pattern", node_size_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Pattern, as.character(pancreasSCE$Pattern))
expect_equal(p$data$CellType, pancreasSCE$CellType)
expect_equal(p$data$Area, pancreasSCE$Area)
cur_sce <- pancreasSCE
cur_sce$ImageNb <- as.factor(cur_sce$ImageNb)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
cur_sce <- pancreasSCE
cur_sce$ImageNb <- as.numeric(cur_sce$ImageNb)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
node_color_fix = "red")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_color_fix = "red")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_color_fix = 1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_shape_by = "ImageNb",
node_shape_fix = "+")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_shape_fix = "+")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_shape_by = "ImageNb",
node_shape_fix = 21)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_shape_fix = 21)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_size_by = "Area",
node_size_fix = 5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_size_fix = 5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
cur_sce <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "knn", k = 3)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType", node_color_by = "PIN",
assay_type = "exprs", node_size_fix = 5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Pattern", node_color_by = "Pattern")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Pattern", node_color_by = "Pattern",
nodes_first = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Area", node_color_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "CellType")
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "Pattern")
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "Area")
expect_s3_class(p, "ggraph")
mcols(colPair(cur_sce, "knn_interaction_graph"))$test <- runif(length(colPair(cur_sce, "knn_interaction_graph")))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "test")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
mcols(colPair(cur_sce, "knn_interaction_graph"))$test_2 <- letters[sample(x = 1:10,
size = length(colPair(cur_sce, "knn_interaction_graph")),
replace = TRUE)]
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "test_2")
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType",
edge_color_fix = "red")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_fix = "red")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_fix = 0.1, edge_width_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_fix = 0.1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p2 <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
directed = FALSE)
expect_s3_class(p2, "ggraph")
expect_silent(print(p2))
expect_equal(p2$data$x, pancreasSCE$Pos_X)
expect_equal(p2$data$y, pancreasSCE$Pos_Y)
expect_equal(p2$data$ImageNb, pancreasSCE$ImageNb)
cur_graph <- igraph::as.igraph(attributes(p$data)$graph)
cur_graph <- igraph::as.undirected(cur_graph)
cur_graph_2 <- igraph::as.igraph(attributes(p2$data)$graph)
cur_edges <- igraph::as_edgelist(cur_graph)
cur_edges_2 <- igraph::as_edgelist(cur_graph_2)
cur_edges <- cur_edges[order(paste(cur_edges[,1], cur_edges[,2])),]
cur_edges_2 <- cur_edges_2[order(paste(cur_edges_2[,1], cur_edges_2[,2])),]
expect_equal(cur_edges, cur_edges_2)
# Delaunay
cur_sce <- buildSpatialGraph(cur_sce, img_id = "ImageNb",
type = "delaunay")
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "delaunay_interaction_graph",
edge_width_fix = 0.1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p2 <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "delaunay_interaction_graph",
directed = FALSE)
expect_s3_class(p2, "ggraph")
expect_silent(print(p2))
expect_equal(p2$data$x, pancreasSCE$Pos_X)
expect_equal(p2$data$y, pancreasSCE$Pos_Y)
expect_equal(p2$data$ImageNb, pancreasSCE$ImageNb)
cur_graph <- igraph::as.igraph(attributes(p$data)$graph)
cur_graph <- igraph::as.undirected(cur_graph)
cur_graph_2 <- igraph::as.igraph(attributes(p2$data)$graph)
cur_edges <- igraph::as_edgelist(cur_graph)
cur_edges_2 <- igraph::as_edgelist(cur_graph_2)
cur_edges <- cur_edges[order(paste(cur_edges[,1], cur_edges[,2])),]
cur_edges_2 <- cur_edges_2[order(paste(cur_edges_2[,1], cur_edges_2[,2])),]
expect_equal(cur_edges, cur_edges_2)
# Expansion
cur_sce <- buildSpatialGraph(cur_sce, img_id = "ImageNb",
type = "expansion", threshold = 15)
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "expansion_interaction_graph",
edge_width_fix = 0.1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p2 <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "expansion_interaction_graph",
directed = FALSE)
expect_s3_class(p2, "ggraph")
expect_silent(print(p2))
expect_equal(p2$data$x, pancreasSCE$Pos_X)
expect_equal(p2$data$y, pancreasSCE$Pos_Y)
expect_equal(p2$data$ImageNb, pancreasSCE$ImageNb)
cur_graph <- igraph::as.igraph(attributes(p$data)$graph)
cur_graph <- igraph::as.undirected(cur_graph)
cur_graph_2 <- igraph::as.igraph(attributes(p2$data)$graph)
cur_edges <- igraph::as_edgelist(cur_graph)
cur_edges_2 <- igraph::as_edgelist(cur_graph_2)
cur_edges <- cur_edges[order(paste(cur_edges[,1], cur_edges[,2])),]
cur_edges_2 <- cur_edges_2[order(paste(cur_edges_2[,1], cur_edges_2[,2])),]
expect_equal(cur_edges, cur_edges_2)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType", node_color_by = "CellType",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Pattern", node_color_by = "Pattern",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Area", node_color_by = "Area",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "CellType",
directed = FALSE)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "Pattern",
directed = FALSE)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "Area",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "test",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "test_2",
directed = FALSE)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType",
edge_color_fix = "red",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_fix = "red",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_fix = 0.1, edge_width_by = "Area",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_fix = 0.1,
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "CellType", edge_color_by = "Area", node_color_by = "CellType",
node_shape_by = "ImageNb", node_size_by = "Area",
directed = TRUE)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(),
directed = TRUE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.1, "inch"), type = "closed"),
directed = TRUE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.1, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.1, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
flip_y = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
flip_x = TRUE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
flip_x = TRUE, flip_y = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
aspect_ratio = 2)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
# making one image smaller
cur_sce_2 <- cur_sce[,cur_sce$ImageNb == "1"]
cur_sce_2 <- cur_sce_2[,cur_sce_2$Pos_X > 30 & cur_sce_2$Pos_Y > 50]
cur_sce_3 <- cur_sce[,cur_sce$ImageNb == "2"]
cur_sce_3 <- cur_sce_3[,cur_sce_3$Pos_X > 30 & cur_sce_3$Pos_Y > 70]
cur_sce_4 <- cbind(cur_sce_2, cur_sce_3, cur_sce[,cur_sce$ImageNb == "3"])
p <- plotSpatial(cur_sce_4, img_id = "ImageName", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
# Testing the aspect_ratio
cur_sce_5 <- cur_sce_4[,cur_sce_4$ImageNb == 1 | cur_sce_4$ImageNb == 2]
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", aspect_ratio = NULL)
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", scales = "free")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", scales = "free", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType")
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", scales = "free")
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", scales = "free", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph")
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", aspect_ratio = 2, scales = "free")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", scales = "free")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", scales = "free", aspect_ratio = NULL)
expect_silent(print(p))
## Subsetting
cur_sce2 <- cur_sce[,cur_sce$Pattern]
p <- plotSpatial(cur_sce2, img_id = "ImageNb", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.05, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE, scales = "fixed", node_size_fix = 0.1, edge_width_fix = 0.5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce2, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", edge_width_by = "CellType",
edge_color_by = "Area", node_color_by = "CellType",
node_shape_by = "ImageNb", node_size_by = "Area",)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce2[,cur_sce2$ImageNb == 2], img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.05, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE, scales = "fixed", node_size_fix = 0.1,
edge_width_fix = 0.5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.05, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE, scales = "free", nrow = 1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.05, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE, scales = "free", ncol = 1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
## Modify plots
p <- plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", node_color_by = "CellType",
node_shape_by = "ImageName", node_size_by = "Area", edge_color_by = "Pattern",
edge_width_by = "Area") +
scale_edge_color_brewer(palette = "Set1") +
scale_color_manual(values = c(celltype_A = "yellow",
celltype_C = "green",
celltype_B = "dark blue")) +
scale_shape_manual(values = c(E34_imc.tiff = 10,
G01_imc.tiff = 12,
J02_imc.tiff = 14)) +
scale_edge_width(range = c(0.1,2)) +
scale_size(range = c(4, 12))
expect_s3_class(p, "ggraph")
expect_silent(print(p))
# SpatialExperiment
library(SpatialExperiment)
cur_spe <- SpatialExperiment(assays = list(counts = counts(cur_sce)),
sample_id = cur_sce$ImageName)
colData(cur_spe) <- colData(cur_sce)
colData(cur_spe)[,c("Pos_X", "Pos_Y")] <- NULL
colPairs(cur_spe) <- colPairs(cur_sce)
# Error
expect_error(p <- plotSpatial(cur_spe, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", node_color_by = "CellType",
node_shape_by = "ImageName", node_size_by = "Area", edge_color_by = "Pattern",
edge_width_by = "Area"), regex = "'coords' not in spatialCoords(object).",
fixed = TRUE)
spatialCoords(cur_spe) <- as.matrix(colData(cur_sce)[,c("Pos_X", "Pos_Y")])
p1 <- plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", node_color_by = "CellType",
node_shape_by = "ImageName", node_size_by = "Area", edge_color_by = "Pattern",
edge_width_by = "Area")
p2 <- plotSpatial(cur_spe, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", node_color_by = "CellType",
node_shape_by = "ImageName", node_size_by = "Area", edge_color_by = "Pattern",
edge_width_by = "Area")
expect_s3_class(p2, "ggraph")
expect_silent(print(p2))
expect_equal(p$data, p2$data, check.attributes = FALSE)
expect_equal(p$layers, p2$layers, check.attributes = FALSE)
expect_equal(p$mapping, p2$mapping, check.attributes = FALSE)
expect_equal(p$theme, p2$theme, check.attributes = FALSE)
expect_equal(p$coordinates, p2$coordinates, check.attributes = FALSE)
expect_equal(p$plot_env, p2$plot_env, check.attributes = FALSE)
expect_equal(p$labels, p2$labels, check.attributes = FALSE)
# Fail
expect_error(plotSpatial("test"), "'object' not of type 'SingleCellExperiment'.")
expect_error(plotSpatial(cur_sce), 'argument "img_id" is missing, with no default')
expect_error(plotSpatial(cur_sce, img_id = "test"), "'img_id' not in colData(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = 1), "'img_id' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", coords = 1),
"'coords' must be a character vector of length 2.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", coords = c(1, 2)),
"'coords' must be a character vector of length 2.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", coords = c("Pos_X", "test")),
"'coords' not in colData(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_spe, img_id = "ImageNb", coords = c("Pos_X", "test")),
"'coords' not in spatialCoords(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = 1),
"'node_color_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = c("test", "test2")),
"'node_color_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "test"),
"'node_color_by' not in colData(object) or rownames(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN"),
"When coloring nodes by marker expression, please specify 'assay_type'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN", assay_type = 1),
"'assay_type' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN", assay_type = "test"),
"'assay_type' not an assay in object.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = c("test", "test2")),
"'node_shape_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = "test"),
"'node_shape_by' not in colData(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = c("test", "test2")),
"'node_size_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = "test"),
"'node_size_by' not in colData(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = "test"),
"'draw_edges' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = c("test", "test2")),
"'draw_edges' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE),
"Please specify the name of the column pairing via 'colPairName'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "test"),
"No column pairing with name test found.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = 1),
"'colPairName' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = c("test", "test2")),
"'colPairName' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
edge_color_by = "test2"),
"'edge_color_by' not in 'colData(object)' or in 'mcols(colPair(object, colPairName))'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
edge_color_by = c("test", "test2")),
"'edge_color_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
edge_width_by = "test2"),
"'edge_width_by' not in 'colData(object)' or in 'mcols(colPair(object, colPairName))'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
edge_width_by = c("test", "test2")),
"'edge_width_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
directed = "test"),
"'directed' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = "test"),
"'arrow' must be of class grid::arrow.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = grid::arrow(),
end_cap = "test"),
"'end_cap' must be of type 'ggraph_geometry'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
nodes_first = "test"),
"'nodes_first' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
ncols = "test"),
"'ncols' must be a single numeric",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
nrows = "test"),
"'nrows' must be a single numeric",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
scales = "test"),
"'scales' should be one of 'fixed', 'free_x', 'free_y', 'free'.",
fixed = TRUE)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
node_color_fix = "test")
expect_error(print(p),
"Unknown colour name: test",
fixed = TRUE)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
node_size_fix = "test")
expect_error(print(p),
"non-numeric argument to binary operator",
fixed = TRUE)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_fix = "test")
expect_error(print(p),
"Unknown colour name: test",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
flip_x = "test"),
"'flip_x' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
flip_x = c(1, 2)),
"'flip_x' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
flip_y = "test"),
"'flip_y' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
flip_y = c(1, 2)),
"'flip_y' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
aspect_ratio = c(1, 2)),
"'aspect_ratio' must be a single positive number, NULL or 'auto'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
aspect_ratio = "test"),
"'aspect_ratio' must be a single positive number, NULL or 'auto'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
aspect_ratio = -1),
"'aspect_ratio' must be a single positive number, NULL or 'auto'.",
fixed = TRUE)
})
BodenmillerGroup/imcRtools documentation built on July 1, 2024, 5:15 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
test_that("plotSpatial function works", {
library(cytomapper)
library(ggraph)
data("pancreasSCE")
cur_sce1 <- pancreasSCE[,pancreasSCE$ImageNb == 1]
cur_sce2 <- pancreasSCE[,pancreasSCE$ImageNb == 2]
cur_sce3 <- pancreasSCE[,pancreasSCE$ImageNb == 3]
cur_sce1$Pos_X <- cur_sce1$Pos_X - min(cur_sce1$Pos_X)
cur_sce1$Pos_Y <- cur_sce1$Pos_Y - min(cur_sce1$Pos_Y)
cur_sce2$Pos_X <- cur_sce2$Pos_X - min(cur_sce2$Pos_X)
cur_sce2$Pos_Y <- cur_sce2$Pos_Y - min(cur_sce2$Pos_Y)
cur_sce3$Pos_X <- cur_sce3$Pos_X - min(cur_sce3$Pos_X)
cur_sce3$Pos_Y <- cur_sce3$Pos_Y - min(cur_sce3$Pos_Y)
pancreasSCE <- cbind(cur_sce1, cur_sce2, cur_sce3)
cur_sce <- pancreasSCE
# SingleCellExperiment
expect_silent(p <- plotSpatial(cur_sce, img_id = "ImageNb"))
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$CellType, pancreasSCE$CellType)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Area, pancreasSCE$Area)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "Pattern")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Pattern, pancreasSCE$Pattern)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN", assay_type = "counts")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$PIN, counts(pancreasSCE)["PIN",], check.attributes = FALSE)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN", assay_type = "exprs")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$PIN, assay(pancreasSCE, "exprs")["PIN",], check.attributes = FALSE)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CDH", assay_type = "exprs")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$CDH, assay(pancreasSCE, "exprs")["CDH",], check.attributes = FALSE)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$CellType, pancreasSCE$CellType)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = "Area")
expect_s3_class(p, "ggraph")
expect_warning(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Area, as.character(pancreasSCE$Area))
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = "Pattern")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Pattern, as.character(pancreasSCE$Pattern))
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = "CellType")
expect_s3_class(p, "ggraph")
#expect_warning(print(p), regexp = "Using size for a discrete variable is not advised.")
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$CellType, pancreasSCE$CellType)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Area, pancreasSCE$Area)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = "Pattern")
expect_s3_class(p, "ggraph")
#expect_warning(print(p), regexp = "Using size for a discrete variable is not advised.")
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Pattern, pancreasSCE$Pattern)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType",
node_shape_by = "Pattern", node_size_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
expect_equal(p$data$Pattern, as.character(pancreasSCE$Pattern))
expect_equal(p$data$CellType, pancreasSCE$CellType)
expect_equal(p$data$Area, pancreasSCE$Area)
cur_sce <- pancreasSCE
cur_sce$ImageNb <- as.factor(cur_sce$ImageNb)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
cur_sce <- pancreasSCE
cur_sce$ImageNb <- as.numeric(cur_sce$ImageNb)
p <- plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
node_color_fix = "red")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_color_fix = "red")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_color_fix = 1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_shape_by = "ImageNb",
node_shape_fix = "+")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_shape_fix = "+")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_shape_by = "ImageNb",
node_shape_fix = 21)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_shape_fix = 21)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_size_by = "Area",
node_size_fix = 5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName",
node_size_fix = 5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
cur_sce <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "knn", k = 3)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
expect_equal(p$data$x, pancreasSCE$Pos_X)
expect_equal(p$data$y, pancreasSCE$Pos_Y)
expect_equal(p$data$ImageNb, pancreasSCE$ImageNb)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType", node_color_by = "PIN",
assay_type = "exprs", node_size_fix = 5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Pattern", node_color_by = "Pattern")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Pattern", node_color_by = "Pattern",
nodes_first = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Area", node_color_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "CellType")
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "Pattern")
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "Area")
expect_s3_class(p, "ggraph")
mcols(colPair(cur_sce, "knn_interaction_graph"))$test <- runif(length(colPair(cur_sce, "knn_interaction_graph")))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "test")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
mcols(colPair(cur_sce, "knn_interaction_graph"))$test_2 <- letters[sample(x = 1:10,
size = length(colPair(cur_sce, "knn_interaction_graph")),
replace = TRUE)]
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "test_2")
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType",
edge_color_fix = "red")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_fix = "red")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_fix = 0.1, edge_width_by = "Area")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_fix = 0.1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p2 <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
directed = FALSE)
expect_s3_class(p2, "ggraph")
expect_silent(print(p2))
expect_equal(p2$data$x, pancreasSCE$Pos_X)
expect_equal(p2$data$y, pancreasSCE$Pos_Y)
expect_equal(p2$data$ImageNb, pancreasSCE$ImageNb)
cur_graph <- igraph::as.igraph(attributes(p$data)$graph)
cur_graph <- igraph::as.undirected(cur_graph)
cur_graph_2 <- igraph::as.igraph(attributes(p2$data)$graph)
cur_edges <- igraph::as_edgelist(cur_graph)
cur_edges_2 <- igraph::as_edgelist(cur_graph_2)
cur_edges <- cur_edges[order(paste(cur_edges[,1], cur_edges[,2])),]
cur_edges_2 <- cur_edges_2[order(paste(cur_edges_2[,1], cur_edges_2[,2])),]
expect_equal(cur_edges, cur_edges_2)
# Delaunay
cur_sce <- buildSpatialGraph(cur_sce, img_id = "ImageNb",
type = "delaunay")
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "delaunay_interaction_graph",
edge_width_fix = 0.1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p2 <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "delaunay_interaction_graph",
directed = FALSE)
expect_s3_class(p2, "ggraph")
expect_silent(print(p2))
expect_equal(p2$data$x, pancreasSCE$Pos_X)
expect_equal(p2$data$y, pancreasSCE$Pos_Y)
expect_equal(p2$data$ImageNb, pancreasSCE$ImageNb)
cur_graph <- igraph::as.igraph(attributes(p$data)$graph)
cur_graph <- igraph::as.undirected(cur_graph)
cur_graph_2 <- igraph::as.igraph(attributes(p2$data)$graph)
cur_edges <- igraph::as_edgelist(cur_graph)
cur_edges_2 <- igraph::as_edgelist(cur_graph_2)
cur_edges <- cur_edges[order(paste(cur_edges[,1], cur_edges[,2])),]
cur_edges_2 <- cur_edges_2[order(paste(cur_edges_2[,1], cur_edges_2[,2])),]
expect_equal(cur_edges, cur_edges_2)
# Expansion
cur_sce <- buildSpatialGraph(cur_sce, img_id = "ImageNb",
type = "expansion", threshold = 15)
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "expansion_interaction_graph",
edge_width_fix = 0.1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p2 <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "expansion_interaction_graph",
directed = FALSE)
expect_s3_class(p2, "ggraph")
expect_silent(print(p2))
expect_equal(p2$data$x, pancreasSCE$Pos_X)
expect_equal(p2$data$y, pancreasSCE$Pos_Y)
expect_equal(p2$data$ImageNb, pancreasSCE$ImageNb)
cur_graph <- igraph::as.igraph(attributes(p$data)$graph)
cur_graph <- igraph::as.undirected(cur_graph)
cur_graph_2 <- igraph::as.igraph(attributes(p2$data)$graph)
cur_edges <- igraph::as_edgelist(cur_graph)
cur_edges_2 <- igraph::as_edgelist(cur_graph_2)
cur_edges <- cur_edges[order(paste(cur_edges[,1], cur_edges[,2])),]
cur_edges_2 <- cur_edges_2[order(paste(cur_edges_2[,1], cur_edges_2[,2])),]
expect_equal(cur_edges, cur_edges_2)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType", node_color_by = "CellType",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Pattern", node_color_by = "Pattern",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "Area", node_color_by = "Area",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "CellType",
directed = FALSE)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "Pattern",
directed = FALSE)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "Area",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "test",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "test_2",
directed = FALSE)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_by = "CellType",
edge_color_fix = "red",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_fix = "red",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_fix = 0.1, edge_width_by = "Area",
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_fix = 0.1,
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_width_by = "CellType", edge_color_by = "Area", node_color_by = "CellType",
node_shape_by = "ImageNb", node_size_by = "Area",
directed = TRUE)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(),
directed = TRUE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.1, "inch"), type = "closed"),
directed = TRUE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.1, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.1, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
flip_y = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
flip_x = TRUE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
flip_x = TRUE, flip_y = FALSE)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageName", node_color_by = "CellType",
aspect_ratio = 2)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
# making one image smaller
cur_sce_2 <- cur_sce[,cur_sce$ImageNb == "1"]
cur_sce_2 <- cur_sce_2[,cur_sce_2$Pos_X > 30 & cur_sce_2$Pos_Y > 50]
cur_sce_3 <- cur_sce[,cur_sce$ImageNb == "2"]
cur_sce_3 <- cur_sce_3[,cur_sce_3$Pos_X > 30 & cur_sce_3$Pos_Y > 70]
cur_sce_4 <- cbind(cur_sce_2, cur_sce_3, cur_sce[,cur_sce$ImageNb == "3"])
p <- plotSpatial(cur_sce_4, img_id = "ImageName", node_color_by = "CellType")
expect_s3_class(p, "ggraph")
expect_silent(print(p))
# Testing the aspect_ratio
cur_sce_5 <- cur_sce_4[,cur_sce_4$ImageNb == 1 | cur_sce_4$ImageNb == 2]
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", aspect_ratio = NULL)
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", scales = "free")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", scales = "free", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType")
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", scales = "free")
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", scales = "free", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph")
expect_silent(print(p))
p <- plotSpatial(cur_sce_3, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", aspect_ratio = 2)
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", aspect_ratio = 2, scales = "free")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", scales = "free")
expect_silent(print(p))
p <- plotSpatial(cur_sce_5, img_id = "ImageName", node_color_by = "CellType", draw_edges = TRUE, colPairName = "knn_interaction_graph", scales = "free", aspect_ratio = NULL)
expect_silent(print(p))
## Subsetting
cur_sce2 <- cur_sce[,cur_sce$Pattern]
p <- plotSpatial(cur_sce2, img_id = "ImageNb", draw_edges = TRUE, colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.05, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE, scales = "fixed", node_size_fix = 0.1, edge_width_fix = 0.5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce2, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", edge_width_by = "CellType",
edge_color_by = "Area", node_color_by = "CellType",
node_shape_by = "ImageNb", node_size_by = "Area",)
expect_s3_class(p, "ggraph")
p <- plotSpatial(cur_sce2[,cur_sce2$ImageNb == 2], img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.05, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE, scales = "fixed", node_size_fix = 0.1,
edge_width_fix = 0.5)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.05, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE, scales = "free", nrow = 1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
p <- plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = arrow(angle = 10, length = unit(0.05, "inch"), type = "closed"),
end_cap = circle(0.3, "cm"),
directed = TRUE, scales = "free", ncol = 1)
expect_s3_class(p, "ggraph")
expect_silent(print(p))
## Modify plots
p <- plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", node_color_by = "CellType",
node_shape_by = "ImageName", node_size_by = "Area", edge_color_by = "Pattern",
edge_width_by = "Area") +
scale_edge_color_brewer(palette = "Set1") +
scale_color_manual(values = c(celltype_A = "yellow",
celltype_C = "green",
celltype_B = "dark blue")) +
scale_shape_manual(values = c(E34_imc.tiff = 10,
G01_imc.tiff = 12,
J02_imc.tiff = 14)) +
scale_edge_width(range = c(0.1,2)) +
scale_size(range = c(4, 12))
expect_s3_class(p, "ggraph")
expect_silent(print(p))
# SpatialExperiment
library(SpatialExperiment)
cur_spe <- SpatialExperiment(assays = list(counts = counts(cur_sce)),
sample_id = cur_sce$ImageName)
colData(cur_spe) <- colData(cur_sce)
colData(cur_spe)[,c("Pos_X", "Pos_Y")] <- NULL
colPairs(cur_spe) <- colPairs(cur_sce)
# Error
expect_error(p <- plotSpatial(cur_spe, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", node_color_by = "CellType",
node_shape_by = "ImageName", node_size_by = "Area", edge_color_by = "Pattern",
edge_width_by = "Area"), regex = "'coords' not in spatialCoords(object).",
fixed = TRUE)
spatialCoords(cur_spe) <- as.matrix(colData(cur_sce)[,c("Pos_X", "Pos_Y")])
p1 <- plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", node_color_by = "CellType",
node_shape_by = "ImageName", node_size_by = "Area", edge_color_by = "Pattern",
edge_width_by = "Area")
p2 <- plotSpatial(cur_spe, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph", node_color_by = "CellType",
node_shape_by = "ImageName", node_size_by = "Area", edge_color_by = "Pattern",
edge_width_by = "Area")
expect_s3_class(p2, "ggraph")
expect_silent(print(p2))
expect_equal(p$data, p2$data, check.attributes = FALSE)
expect_equal(p$layers, p2$layers, check.attributes = FALSE)
expect_equal(p$mapping, p2$mapping, check.attributes = FALSE)
expect_equal(p$theme, p2$theme, check.attributes = FALSE)
expect_equal(p$coordinates, p2$coordinates, check.attributes = FALSE)
expect_equal(p$plot_env, p2$plot_env, check.attributes = FALSE)
expect_equal(p$labels, p2$labels, check.attributes = FALSE)
# Fail
expect_error(plotSpatial("test"), "'object' not of type 'SingleCellExperiment'.")
expect_error(plotSpatial(cur_sce), 'argument "img_id" is missing, with no default')
expect_error(plotSpatial(cur_sce, img_id = "test"), "'img_id' not in colData(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = 1), "'img_id' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", coords = 1),
"'coords' must be a character vector of length 2.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", coords = c(1, 2)),
"'coords' must be a character vector of length 2.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", coords = c("Pos_X", "test")),
"'coords' not in colData(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_spe, img_id = "ImageNb", coords = c("Pos_X", "test")),
"'coords' not in spatialCoords(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = 1),
"'node_color_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = c("test", "test2")),
"'node_color_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "test"),
"'node_color_by' not in colData(object) or rownames(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN"),
"When coloring nodes by marker expression, please specify 'assay_type'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN", assay_type = 1),
"'assay_type' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "PIN", assay_type = "test"),
"'assay_type' not an assay in object.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = c("test", "test2")),
"'node_shape_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_shape_by = "test"),
"'node_shape_by' not in colData(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = c("test", "test2")),
"'node_size_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", node_size_by = "test"),
"'node_size_by' not in colData(object).",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = "test"),
"'draw_edges' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = c("test", "test2")),
"'draw_edges' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE),
"Please specify the name of the column pairing via 'colPairName'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "test"),
"No column pairing with name test found.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = 1),
"'colPairName' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = c("test", "test2")),
"'colPairName' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
edge_color_by = "test2"),
"'edge_color_by' not in 'colData(object)' or in 'mcols(colPair(object, colPairName))'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
edge_color_by = c("test", "test2")),
"'edge_color_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
edge_width_by = "test2"),
"'edge_width_by' not in 'colData(object)' or in 'mcols(colPair(object, colPairName))'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
edge_width_by = c("test", "test2")),
"'edge_width_by' must be a single string.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
directed = "test"),
"'directed' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = "test"),
"'arrow' must be of class grid::arrow.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb", draw_edges = TRUE,
colPairName = "knn_interaction_graph",
arrow = grid::arrow(),
end_cap = "test"),
"'end_cap' must be of type 'ggraph_geometry'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
nodes_first = "test"),
"'nodes_first' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
ncols = "test"),
"'ncols' must be a single numeric",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
nrows = "test"),
"'nrows' must be a single numeric",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
scales = "test"),
"'scales' should be one of 'fixed', 'free_x', 'free_y', 'free'.",
fixed = TRUE)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
node_color_fix = "test")
expect_error(print(p),
"Unknown colour name: test",
fixed = TRUE)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
node_size_fix = "test")
expect_error(print(p),
"non-numeric argument to binary operator",
fixed = TRUE)
p <- plotSpatial(cur_sce, img_id = "ImageNb",
draw_edges = TRUE, colPairName = "knn_interaction_graph",
edge_color_fix = "test")
expect_error(print(p),
"Unknown colour name: test",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
flip_x = "test"),
"'flip_x' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
flip_x = c(1, 2)),
"'flip_x' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
flip_y = "test"),
"'flip_y' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
flip_y = c(1, 2)),
"'flip_y' must be a single logical",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
aspect_ratio = c(1, 2)),
"'aspect_ratio' must be a single positive number, NULL or 'auto'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
aspect_ratio = "test"),
"'aspect_ratio' must be a single positive number, NULL or 'auto'.",
fixed = TRUE)
expect_error(plotSpatial(cur_sce, img_id = "ImageNb",
aspect_ratio = -1),
"'aspect_ratio' must be a single positive number, NULL or 'auto'.",
fixed = TRUE)
})
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.