R/spatial_clusters.R
spatialSplitCluster.Rd
Split cluster annotations based on a spatial network
spatialSplitCluster(
gobject,
spat_unit = NULL,
feat_type = NULL,
spatial_network_name = "Delaunay_network",
cluster_col,
split_clus_name = paste0(cluster_col, "_split"),
include_all_ids = TRUE,
missing_id_name = "not_connected",
return_gobject = TRUE
)
giotto object
spatial unit (e.g. "cell")
feature type (e.g. "rna", "dna", "protein")
character. Name of spatial network to use
character. Column in metadata containing original clustering
character. Name to assign the split cluster results
Boolean. Include all ids, including vertex ids not found in the spatial network
Character. Name for vertices that were missing from spatial network
Boolean. Return giotto object
giotto object with cluster annotations
library(Giotto)
g <- GiottoData::loadGiottoMini("vizgen")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#>
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/bin/python3"
activeSpatUnit(g) <- "aggregate"
spatPlot2D(g, cell_color = "leiden_clus")
g <- spatialSplitCluster(g,
cluster_col = "leiden_clus",
split_clus_name = "new"
)
#> Error in V(g): could not find function "V"
# don't show legend since there are too many categories generated
spatPlot2D(g, cell_color = "new", show_legend = FALSE)
#> Error in (function (ggobject, instrs = NULL, sdimx = NULL, sdimy = NULL, cell_locations_metadata_selected, cell_locations_metadata_other, cell_color = NULL, color_as_factor = TRUE, cell_color_code = NULL, cell_color_gradient = NULL, gradient_midpoint = NULL, gradient_style = "divergent", gradient_limits = NULL, select_cell_groups = NULL, select_cells = NULL, point_size = 2, point_alpha = 1, point_border_col = "lightgrey", point_border_stroke = 0.1, show_cluster_center = FALSE, show_center_label = TRUE, center_point_size = 4, center_point_border_col = "black", center_point_border_stroke = 0.1, label_size = 4, label_fontface = "bold", show_other_cells = TRUE, other_cell_color = "lightgrey", other_point_size = 1, show_legend = TRUE) { if (is.null(sdimx) || is.null(sdimy)) { warning(wrap_txt("plot_method = ggplot,\n but spatial dimensions for sdimx and/or sdimy\n are not specified. It will default to the\n 'sdimx' and 'sdimy' ")) sdimx <- "sdimx" sdimy <- "sdimy" } point_size <- as.numeric(point_size) point_alpha <- as.numeric(point_alpha) point_border_stroke <- as.numeric(point_border_stroke) center_point_size <- as.numeric(center_point_size) center_point_border_stroke <- as.numeric(center_point_border_stroke) label_size <- as.numeric(label_size) other_point_size <- as.numeric(other_point_size) pl <- ggobject if ((!is.null(select_cells) || !is.null(select_cell_groups)) && isTRUE(show_other_cells)) { pl <- pl + ggplot2::geom_point(data = cell_locations_metadata_other, aes_string(x = sdimx, sdimy), color = other_cell_color, show.legend = FALSE, size = other_point_size, alpha = point_alpha) } if (is.null(cell_color)) { cell_color <- "lightblue" pl <- pl + ggplot2::geom_point(data = cell_locations_metadata_selected, aes_string(x = sdimx, y = sdimy), show.legend = show_legend, shape = 21, fill = cell_color, size = point_size, stroke = point_border_stroke, color = point_border_col, alpha = point_alpha) } else if (length(cell_color) > 1L) { if (is.numeric(cell_color) || is.factor(cell_color)) { if (nrow(cell_locations_metadata_selected) != length(cell_color)) { stop("\n vector needs to be the same lengths as\n number of cells \n") } cell_locations_metadata_selected[["temp_color"]] <- cell_color pl <- pl + ggplot2::geom_point(data = cell_locations_metadata_selected, aes_string2(x = sdimx, y = sdimy, fill = "temp_color"), show.legend = show_legend, shape = 21, size = point_size, color = point_border_col, stroke = point_border_stroke, alpha = point_alpha) } else if (is.character(cell_color)) { if (!all(cell_color %in% grDevices::colors())) { stop("cell_color is not numeric,\n a factor or vector of colors \n") } pl <- pl + ggplot2::geom_point(data = cell_locations_metadata_selected, aes_string2(x = sdimx, y = sdimy), show.legend = show_legend, shape = 21, fill = cell_color, size = point_size, color = point_border_col, stroke = point_border_stroke, alpha = point_alpha) } } else if (is.character(cell_color)) { if (!cell_color %in% colnames(cell_locations_metadata_selected)) { if (!cell_color %in% grDevices::colors()) { stop(cell_color, " is not a color or a column name \n") } pl <- pl + ggplot2::geom_point(data = cell_locations_metadata_selected, aes_string2(x = sdimx, y = sdimy), show.legend = show_legend, shape = 21, fill = cell_color, size = point_size, color = point_border_col, stroke = point_border_stroke, alpha = point_alpha) } else { class_cell_color <- class(cell_locations_metadata_selected[[cell_color]]) if ((class_cell_color %in% c("integer", "numeric")) && !isTRUE(color_as_factor)) { if (!is.null(gradient_limits) && is.vector(gradient_limits) && length(gradient_limits) == 2) { lower_lim <- gradient_limits[[1]] upper_lim <- gradient_limits[[2]] numeric_data <- cell_locations_metadata_selected[[cell_color]] limit_numeric_data <- ifelse(numeric_data > upper_lim, upper_lim, ifelse(numeric_data < lower_lim, lower_lim, numeric_data)) cell_locations_metadata_selected[[cell_color]] <- limit_numeric_data } pl <- pl + ggplot2::geom_point(data = cell_locations_metadata_selected, aes_string2(x = sdimx, y = sdimy, fill = cell_color), show.legend = show_legend, shape = 21, size = point_size, color = point_border_col, stroke = point_border_stroke, alpha = point_alpha) } else { if (isTRUE(color_as_factor)) { factor_data <- factor(cell_locations_metadata_selected[[cell_color]]) cell_locations_metadata_selected[[cell_color]] <- factor_data } if (isTRUE(show_cluster_center) || isTRUE(show_center_label)) { annotated_DT_centers <- cell_locations_metadata_selected[, .(center_1 = stats::median(get("sdimx")), center_2 = stats::median(get("sdimy"))), by = cell_color] factor_center_data <- factor(annotated_DT_centers[[cell_color]]) annotated_DT_centers[[cell_color]] <- factor_center_data } pl <- pl + ggplot2::geom_point(data = cell_locations_metadata_selected, aes_string2(x = sdimx, y = sdimy, fill = cell_color), show.legend = show_legend, shape = 21, size = point_size, color = point_border_col, stroke = point_border_stroke, alpha = point_alpha) if (isTRUE(show_cluster_center) && (isTRUE(color_as_factor) || class_cell_color %in% c("character", "factor"))) { pl <- pl + ggplot2::geom_point(data = annotated_DT_centers, aes_string2(x = "center_1", y = "center_2", fill = cell_color), color = center_point_border_col, stroke = center_point_border_stroke, size = center_point_size, shape = 21, alpha = point_alpha) } if (isTRUE(show_center_label)) { pl <- pl + ggrepel::geom_text_repel(data = annotated_DT_centers, aes_string2(x = "center_1", y = "center_2", label = cell_color), size = label_size, fontface = label_fontface) } } if (!is.null(cell_color_code)) { pl <- pl + ggplot2::scale_fill_manual(values = cell_color_code) } else if (isTRUE(color_as_factor)) { number_colors <- length(unique(factor_data)) cell_color_code <- set_default_color_discrete_cell(instrs = instrs)(n = number_colors) names(cell_color_code) <- unique(factor_data) pl <- pl + ggplot2::scale_fill_manual(values = cell_color_code) } else if (!isTRUE(color_as_factor)) { if (is.null(gradient_midpoint)) { gradient_midpoint <- stats::median(cell_locations_metadata_selected[[cell_color]]) } pl <- pl + set_default_color_continuous_cell(colors = cell_color_gradient, instrs = instrs, style = gradient_style, midpoint = gradient_midpoint, type = "fill", ) } } } return(pl)})(ggobject = structure(list(data = structure(list(), class = "waiver"), layers = list(), scales = <environment>, guides = <environment>, mapping = structure(list(), names = character(0), class = "uneval"), theme = structure(list(line = structure(list(colour = "black", linewidth = 0.5, linetype = 1, lineend = "butt", arrow = FALSE, inherit.blank = TRUE), class = c("element_line", "element" )), rect = structure(list(fill = "white", colour = "black", linewidth = 0.5, linetype = 1, inherit.blank = TRUE), class = c("element_rect", "element")), text = 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326.05385212392), leiden_clus = c(4, 2, 1, 1, 2, 3, 2, 1, 2, 1, 1, 1, 1, 3, 3, 1, 2, 1, 4, 2, 1, 1, 1, 1, 3, 3, 2, 3, 5, 2, 1, 5, 2, 4, 1, 3, 1, 2, 1, 2, 4, 3, 3, 4, 1, 3, 4, 2, 3, 1, 1, 3, 2, 1, 2, 2, 1, 2, 3, 4, 3, 1, 3, 2, 3, 1, 2, 4, 1, 1, 2, 4, 2, 3, 2, 1, 4, 2, 1, 4, 1, 2, 3, 2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 3, 1, 2, 3, 1, 3, 3, 3, 2, 3, 4, 1, 2, 2, 1, 4, 1, 1, 2, 2, 2, 2, 4, 4, 4, 3, 4, 2, 3, 2, 4, 4, 1, 1, 2, 4, 2, 4, 4, 3, 3, 2, 4, 3, 3, 4, 5, 1, 4, 2, 1, 4, 2, 3, 2, 1, 1, 2, 1, 3, 1, 1, 3, 4, 3, 1, 1, 2, 2, 4, 3, 4, 1, 4, 1, 2, 1, 1, 2, 1, 2, 4, 2, 1, 4, 4, 1, 3, 3, 1, 2, 1, 2, 2, 4, 4, 3, 5, 2, 1, 1, 2, 1, 1, 3, 3, 2, 3, 1, 2, 2, 1, 1, 2, 3, 1, 3, 1, 3, 2, 1, 3, 5, 4, 2, 4, 4, 1, 3, 2, 1, 3, 1, 3, 2, 3, 3, 4, 3, 2, 4, 2, 1, 1, 3, 1, 4, 4, 4, 5, 4, 2, 4, 3, 4, 2, 4, 1, 3, 3, 1, 3, 2, 5, 2, 2, 1, 3, 4, 1, 2, 4, 2, 1, 1, 3, 2, 1, 1, 3, 1, 1, 3, 2, 3, 2, 1, 2, 2, 4, 1, 1, 1, 2, 3, 4, 1, 1, 3, 1, 2, 4, 3, 3, 4, 1, 3, 3, 1, 2, 3, 2, 4, 3, 1, 4, 5, 3, 1, 4, 2, 4, 3, 3, 2, 1, 2, 4, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 1, 4, 3, 4, 4, 2, 1, 2, 3, 4, 1, 2, 1, 4, 5, 1, 1, 3, 2, 1, 4, 3, 3, 1, 3, 5, 1, 2, 3, 4, 3, 3, 3, 2, 2, 1, 1, 5, 2, 4, 1, 4, 1, 3, 1, 5, 1, 2, 2, 3, 3, 5, 2, 2, 1, 2, 4, 1, 2, 3, 4, 4, 1, 3, 1, 3, 3, 2, 2, 2, 2, 1, 3, 2, 4, 3, 4, 5, 1, 1, 1, 1, 2, 3, 1, 1, 2, 2, 5, 4, 1, 2, 5, 4, 2, 4, 1, 1, 1, 1, 2, 1, 1, 5, 2, 5, 1, 2, 4, 3, 2, 2, 2, 3, 1, 2, 1, 1, 2, 1, 2, 4, 4, 4, 2, 2, 4, 3, 1), louvain_clus = c(15, 10, 22, 24, 0, 13, 3, 2, 3, 21, 19, 21, 21, 13, 28, 2, 10, 24, 8, 11, 22, 21, 21, 24, 13, 21, 18, 4, 6, 3, 2, 6, 14, 15, 21, 12, 21, 0, 24, 3, 9, 12, 28, 9, 29, 20, 9, 0, 13, 2, 22, 4, 18, 21, 3, 0, 21, 0, 20, 9, 23, 24, 28, 18, 16, 24, 10, 8, 27, 29, 10, 15, 3, 28, 3, 27, 15, 11, 21, 8, 24, 1, 20, 18, 24, 14, 5, 24, 27, 29, 7, 8, 9, 8, 7, 16, 24, 14, 4, 19, 28, 13, 16, 5, 4, 9, 24, 5, 0, 2, 9, 26, 26, 10, 11, 1, 14, 7, 17, 15, 13, 7, 14, 28, 5, 7, 7, 27, 22, 14, 9, 14, 7, 17, 28, 23, 14, 17, 4, 28, 8, 6, 2, 17, 5, 19, 8, 14, 28, 18, 19, 26, 3, 24, 23, 26, 26, 28, 7, 16, 4, 26, 10, 10, 9, 4, 17, 2, 8, 27, 0, 26, 21, 3, 2, 11, 17, 0, 26, 17, 7, 29, 13, 28, 24, 14, 2, 0, 5, 7, 8, 12, 6, 10, 21, 21, 3, 21, 21, 28, 20, 18, 12, 21, 10, 3, 24, 23, 5, 13, 19, 28, 24, 28, 0, 27, 28, 6, 15, 0, 8, 7, 27, 16, 3, 2, 12, 2, 16, 3, 13, 16, 15, 28, 5, 8, 0, 25, 21, 20, 24, 17, 8, 7, 6, 15, 0, 17, 16, 15, 3, 9, 25, 16, 20, 24, 4, 14, 6, 10, 3, 21, 16, 17, 21, 10, 8, 18, 24, 23, 4, 3, 21, 2, 16, 19, 24, 12, 18, 28, 5, 27, 14, 0, 8, 26, 21, 2, 14, 16, 15, 25, 24, 16, 21, 5, 17, 12, 16, 15, 24, 12, 28, 24, 14, 12, 10, 7, 12, 24, 7, 6, 13, 19, 7, 5, 8, 23, 28, 5, 24, 0, 7, 5, 19, 1, 13, 14, 12, 4, 22, 10, 2, 27, 9, 16, 8, 9, 18, 19, 1, 28, 8, 19, 0, 22, 15, 6, 19, 26, 20, 10, 21, 15, 28, 16, 21, 16, 6, 22, 14, 12, 7, 12, 16, 16, 14, 18, 2, 24, 6, 3, 15, 19, 17, 26, 13, 21, 6, 2, 14, 11, 28, 16, 6, 11, 1, 26, 3, 9, 19, 5, 13, 17, 8, 29, 28, 24, 16, 13, 5, 0, 5, 10, 24, 12, 11, 15, 20, 7, 6, 21, 25, 2, 22, 3, 23, 2, 23, 0, 11, 6, 17, 2, 0, 6, 9, 18, 15, 22, 26, 24, 21, 3, 21, 27, 6, 3, 6, 27, 5, 15, 28, 3, 0, 3, 4, 29, 0, 21, 2, 11, 2, 11, 9, 7, 17, 3, 5, 15, 13, 26), sdimx = c(6637.8808812838, 6471.97820589227, 6801.60964850244, 6789.05500292697, 6807.65042853937, 6823.00666161112, 6714.59974529393, 6893.67783391626, 6553.150314616, 6820.08645751904, 6710.3427827623, 6739.78164732464, 6789.48587843314, 6778.54269420933, 6844.85239392872, 6898.05484110887, 6456.65141488127, 6757.4307452351, 6543.67833565009, 6572.06455004792, 6771.80635804563, 6759.5864935999, 6752.30540722853, 6775.25860580127, 6898.72948587473, 6823.30553732925, 6835.93295576951, 6808.32562760623, 6807.59540821274, 6626.74053986698, 6785.48528357164, 6860.1753773801, 6522.97161083555, 6708.60071737893, 6749.98064221693, 6839.38412177152, 6765.85070030091, 6799.28167698505, 6749.75681156924, 6718.69339489712, 6479.53753434238, 6760.63434678639, 6768.56273348601, 6510.6756138787, 6784.06721565658, 6798.53565464916, 6517.32762826806, 6731.51009836197, 6870.42074123265, 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