R/cell-size.r

In JohnReid/DeLorean: Estimates Pseudotimes for Single Cell Expression Data

#' Estimate the cell sizes according to Anders & Huber
#' Differential expression analysis for sequence count data
#'
#' @param expr.l Melted expression values.
#'
anders.huber.cell.sizes <- function(expr.l) expr.l %>%
  group_by(gene) %>%
  dplyr::summarise(mu=mean(x)) %>%
  left_join(expr.l) %>%
  group_by(cell) %>%
  dplyr::summarise(S.hat=median(x-mu))


#' Estimate the cell sizes. We only consider genes that are expressed in
#' a certain proportion of cells.
#'
#' @param dl de.lorean object.
#' @param cell.prop The proportion of cells a gene must be expressed in to be
#'   considered for cell size estimation
#' @param expr.threshold The threshold above which we consider a gene to be expressed
#' @param by.capture Estimate the cell sizes by considering the cells at each
#'   capture time separately
#'
#' @export
#'
estimate.cell.sizes <- function(dl, cell.prop=.5, expr.threshold=0, by.capture=TRUE) within(dl, {
  expr.l <- melt.expr(dl)
  expressed.genes <-
    expr.l %>%
    group_by(gene) %>%
    dplyr::summarise(prop.expr=mean(x>expr.threshold)) %>%
    filter(prop.expr > cell.prop)
  if (by.capture) {
    cell.sizes <-
      expressed.genes %>%
      left_join(expr.l) %>%
      left_join(cell.meta) %>%
      group_by(capture) %>%
      do(anders.huber.cell.sizes(.))
  } else {
    cell.sizes <- anders.huber.cell.sizes(expressed.genes %>% left_join(expr.l))
  }
})


#' Adjust the expression by the estimated cell sizes.
#'
#' @param dl de.lorean object.
#'
#' @export
#'
adjust.by.cell.sizes <- function(dl) within(dl, {
  expr.before.adj <- expr
  expr.l <- expr.l %>% left_join(cell.sizes) %>% mutate(x=x-S.hat)
  expr <- cast.expr(expr.l)
})