Created
August 31, 2024 17:05
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| library(plotly) | |
| library(ggplot2) | |
| library(XenSCE) | |
| if (!exists("gbm")) load("gbm.rda") | |
| plotly_seg = function(xsce, xlim=c(5800,6000), ylim=c(6300, 6500), 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], ] | |
| 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) -> uu | |
| ggplotly(uu) | |
| } |
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