plotly_seg.R

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)
}