Commit 87eb1899 authored by Lucy McNeill's avatar Lucy McNeill
Browse files

package running with no errors or warnings with devtools

parent 0e696392
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......@@ -2,7 +2,7 @@
#'
#' crop an image around each viable cell candidate.
#' @importFrom stats median sd
#' @importFrom EBImage bwlabel channel colorLabels computeFeatures computeFeatures.basic computeFeatures.moment computeFeatures.shape display filter2 makeBrush readImage rgbImage rmObjects rotate writeImage
#' @importFrom EBImage bwlabel channel colorLabels computeFeatures computeFeatures.basic computeFeatures.moment computeFeatures.shape display filter2 makeBrush readImage rgbImage rmObjects rotate writeImage watershed
#' @importFrom graphics text
#' @importFrom utils str
#' @export auto_crop_fast
......@@ -19,7 +19,11 @@
#' @param brush_size_blob, Brush size for smudging the dna channel to make blobs
#' @param cell_aspect_ratio Maximum aspect ratio of blob to be defined as a cell
#' @param sigma_blob, Sigma in Gaussian brush for smudging the dna channel to make blobs
#' @param channel1_string String appended to the files showing the channel illuminating foci. Defaults to MLH3
#' @param channel2_string String appended to the files showing the channel illuminating synaptonemal complexes. Defaults to SYCP3
#' @param channel3_string Optional. String appended to the files showing the channel illuminating cell structures. Defaults to DAPI, if third channel == "on".
#' @param third_channel Optional, defaults to "off".
#' @param file_ext file extension of your images e.g. tif jpeg or png.
#' @return cropped SC and foci channels around single cells, regardless of stage
......@@ -151,8 +155,11 @@ print("viable cells")
#' @param annotation, Choice to output pipeline choices (recommended to knit)
#' @param file_base, filename base common to all three channels i.e. without -MLH3.jpeg etc.
#' @param img_path, path containing image data to analyse
#'
#' @param channel1_string String appended to the files showing the channel illuminating foci. Defaults to MLH3
#' @param channel2_string String appended to the files showing the channel illuminating synaptonemal complexes. Defaults to SYCP3
#' @param channel3_string Optional. String appended to the files showing the channel illuminating cell structures. Defaults to DAPI, if third channel == "on".
#' @param third_channel Optional, defaults to "off".
#' @param file_ext file extension of your images e.g. tif jpeg or png.
......
......@@ -50,6 +50,16 @@ auto_crop_fast(
\item{sigma_blob, }{Sigma in Gaussian brush for smudging the dna channel to make blobs}
\item{channel3_string}{Optional. String appended to the files showing the channel illuminating cell structures. Defaults to DAPI, if third channel == "on".}
\item{channel2_string}{String appended to the files showing the channel illuminating synaptonemal complexes. Defaults to SYCP3}
\item{channel1_string}{String appended to the files showing the channel illuminating foci. Defaults to MLH3}
\item{file_ext}{file extension of your images e.g. tif jpeg or png.}
\item{third_channel}{Optional, defaults to "off".}
\item{cell_aspect_ratio}{Maximum aspect ratio of blob to be defined as a cell}
}
\value{
......
......@@ -63,6 +63,16 @@ crop_single_object_fast(
\item{cx}{centre of blob x}
\item{cy}{centre of blob y}
\item{channel3_string}{Optional. String appended to the files showing the channel illuminating cell structures. Defaults to DAPI, if third channel == "on".}
\item{channel2_string}{String appended to the files showing the channel illuminating synaptonemal complexes. Defaults to SYCP3}
\item{channel1_string}{String appended to the files showing the channel illuminating foci. Defaults to MLH3}
\item{file_ext}{file extension of your images e.g. tif jpeg or png.}
\item{third_channel}{Optional, defaults to "off".}
}
\value{
Crops around all candidates in both channels
......
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