magickCell: Funcion copada para mostrar fotos de Cell-ID basada en magick
In gerbeldo/tidycell: CellID Data Analysis Inside the Tidyverse

magickCell

R Documentation

Funcion copada para mostrar fotos de Cell-ID basada en magick

Description

El uso más básico es magickCell(cdata=cell.data$data, paths=cell.data$images).

Para mostrar algunas celulas en particular, solo hay que pasarle un cdata filtrado.

Ver la descripción de argumentos más abajo para aprender sobre las opciones.

Al fondo, en los detalles, hay una descripción de como debería ser el paths dataframe.

Usage

magickCell(
  cdata,
  paths,
  max_composite_size = 1000,
  cell_resize = NULL,
  boxSize = 80,
  n.cells = 25,
  equalize_images = F,
  normalize_images = F,
  ch = "BF.out",
  sortVar = NULL,
  seed = NULL,
  .debug = FALSE,
  return_single_imgs = FALSE,
  return_ucid_df = FALSE,
  annotation_params = list(color = "white", background = "black"),
  stack_vertical_first = FALSE,
  return_raw = FALSE
)

Arguments

`cdata`	A Rcell data.frame (not the object).
`paths`	A paths dataframe with file path, t.frame, position and channel information of each picture.
`max_composite_size`	Maximum size of the final composite image (this resize is applied last) in pixels. 1000 by default.
`cell_resize`	Resize string for the individual cell images (`NULL` translates to `boxSize`x`boxSize` by default).
`boxSize`	Size of the box containing the individual cell images. 50 by default.
`n.cells`	maximum number of cells to display.
`equalize_images`	Use magick's function to "equalize" the image when TRUE (FALSE by default).
`normalize_images`	Use magick's function to "normalize" the image when TRUE (FALSE by default).
`ch`	Name of the CellID channel (BF, BF.out, RFP, etc.). "BF.out" by default.
`sortVar`	Variable name used to sort the rows after sampling if a `seed` was specified. NULL by default, to preserve the original or random sampling order.
`seed`	Seed value for sampling of cell images. NULL by default, to disable sampling.
`.debug`	Print more messages if TRUE.
`return_single_imgs`	If TRUE, return a vector of images instead of a tile.
`return_ucid_df`	If TRUE, return is a list of magick images and ucid dataframes.
`annotation_params`	Set to NULL to skip annotations, or a named list with values for magick::annotate options (one or more of the names "color" "background" "size"). Note that size close to zero can be invisible.
`stack_vertical_first`	Set to TRUE to stack images vertically first (useful when `return_single_imgs = T`).
`return_raw`	Returns loaded images prematurely (i.e. without any processing other than magick::image_read and magick::image_crop).

Details

Paths dataframe structure. Output example from glimpse(paths):

Columns: 6
$ pos     <int> 1
$ t.frame <int> 0
$ channel <chr> "YFP"
$ image   <chr> "picture_filename.tif"
$ path    <chr> "/path/to/directory/with/pictures/"
$ file    <chr> "/path/to/directory/with/pictures/picture_filename.tif"
$ is.out  <lgl> FALSE