Created
September 1, 2024 21:06
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code that uses ggplot and some cell-level summaries on XenSPEP/XenSCE
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| library(plotly) | |
| library(ggplot2) | |
| library(XenSCE) | |
| if (!exists("gbm")) load("gbm.rda") | |
| print.xen_ggprep = function(x, ...) { | |
| cat(sprintf("xen_ggprep instance for %d cells with %d cell boundary vertices.\n", ncol(x$sampd), nrow(x$bounds))) | |
| } | |
| ggprep_seg = function(xsce, xlim=c(5800,6200), ylim=c(6300, 6700), show_tx=TRUE) { | |
| bounds = getCellBoundaries(xsce) | |
| bounds = bounds[bounds$vertex_x > xlim[1] & | |
| bounds$vertex_x < xlim[2] & bounds$vertex_y > ylim[1] & bounds$vertex_y < ylim[2],] | |
| c4 <- as.data.frame(bounds) | |
| #ggplot(c4, aes(x=vertex_x, y=vertex_y, group=cell_id)) + geom_path() -> pas | |
| tx = getTranscripts(xsce) | |
| # tx[which(as.character(tx$cell_id) %in% unique(c4$cell_id)),] -> myt | |
| myt = tx[tx$x_location > xlim[1] & tx$x_location < xlim[2] & | |
| tx$y_location > ylim[1] & tx$y_location < ylim[2], ] | |
| sampd = as.data.frame(SummarizedExperiment::colData(xsce[, unique(c4$cell_id)])) | |
| sizq = cut(sampd$cell_area, c(0, quantile(sampd$cell_area, c(.2,.4,.6,.8)), max(sampd$cell_area)+.01)) | |
| sampd$sizq = sizq | |
| bounds = dplyr::left_join(c4, sampd, by="cell_id") | |
| ans = list(bounds=bounds, txdata=myt) | |
| class(ans) = c("xen_ggprep", "list") | |
| ans | |
| # ggplot(c4, aes(x=vertex_x, y=vertex_y, group=cell_id)) + | |
| # geom_path() + | |
| # geom_point(data=myt, aes(x=x_location, y=y_location, | |
| # text=as.character(feature_name)), size=.05, colour="grey", alpha=.2) | |
| } | |
| ss = ggprep_seg(gbm) | |
| plot.xen_ggprep = function(x, y, ...) { | |
| ggplot(x$bounds, aes(x=vertex_x, y=vertex_y, group=cell_id, colour=sizq, fill=sizq)) + | |
| geom_polygon() + geom_path(colour="black") | |
| } |
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