get_cell_image.cell.data: get_cell_image

In gerbeldo/tidycell: CellID Data Analysis Inside the Tidyverse

get_cell_image

Description

Retrieves the images from single cells in an cell.image object

Usage

## S3 method for class 'cell.data'
get_cell_image(
  X,
  subset = NULL,
  channel.subset = NULL,
  channel = NULL,
  time.course = TRUE,
  group = NULL,
  na.rm = TRUE,
  N = 7,
  select = NULL,
  exclude = NULL,
  qc.filter = TRUE,
  box.size = 20,
  ...
)

Arguments

X	cell.data object or data.frame that specifies the images
subset	logical expression indicating elements or rows to keep. Don't specify channel here.
channel.subset	logical expression to specify which image to retrieve with channel and t.frame variables.
channel	character vector of channels to retrieve. If specified, defines the order of the channels.
time.course	boolean indicating if the desired image montage is a time course (i.e. several images for the same cell)
group	character vector or quoted names of variables who's interaction define the groups from which select N random cells.
na.rm	boolean indicating if NAs should be removed.
N	Number of random cells to select from each group. If NULL all cells are selected
select	character vector defining variables names to be included in the returned cell.image object
exclude	character vector defining variables names to be excluded from the returned cell.image object
qc.filter	a boolean value indicating if the quality control filter should be applied over the data
box.size	size in pixels of the image containing the cells. This specifies the 'radius', i.e. the image will be a square of length 2*box.size+1
...	further arguments for methods

gerbeldo/tidycell documentation built on Aug. 15, 2022, 2:35 p.m.