Commit 0ae9a132 authored by Lucy McNeill's avatar Lucy McNeill
Browse files

update count_foci documentation

parent 842a08cb
No preview for this file type
......@@ -15,8 +15,10 @@
#' @export count_foci
#' @param img_path, path containing crops to analyse
#' @param stage, meiosis stage of interest. Currently count_foci determines
#' this with thresholding/ object properties in the synaptonemal complex channel. But will be
#' classified using ML model in future versions.
#' this with thresholding/ object properties in the synaptonemal complex channel
#' by previosly calling the get_pachytene function.
#' Note that if using this option, the count_foci function requires that the
#' input directory contains a folder called “pachytene” with the crops in it.
#' @param offset_px, Pixel value offset used in thresholding of synaptonemal complex channel
#' @param offset_factor, Pixel value offset used in thresholding of foci channel
#' @param brush_size, size of brush to smooth the foci channel. Should be small
......@@ -198,7 +200,11 @@ annotate_foci_counting <- function(img_file,cell_count,img_orig,img_orig_foci,
#' Defaults to +/+.
#' @param foci_areas pixel area of each foci
#' @param df_cells current data frame
#' @param stage meiotic stage
#' @param stage, meiosis stage of interest. Currently count_foci determines
#' this with thresholding/ object properties in the synaptonemal complex channel
#' by previosly calling the get_pachytene function.
#' Note that if using this option, the count_foci function requires that the
#' input directory contains a folder called “pachytene” with the crops in it.
#' @param foci_per_cell foci count for cell
#' @param image_mat matrix with all pixel values above zero
#' @param percent_px percentage of foci mask that coincides with strand channel
......@@ -358,7 +364,11 @@ make_foci_mask <- function(offset_factor,bg,crowded_foci,img_orig_foci,
#' creates strand mask for strand channel crop
#'
#' @param offset_px, Pixel value offset used in thresholding of synaptonemal complex channel
#' @param stage meitoic stage, currently pachytene or not.
#' @param stage, meiosis stage of interest. Currently count_foci determines
#' this with thresholding/ object properties in the synaptonemal complex channel
#' by previosly calling the get_pachytene function.
#' Note that if using this option, the count_foci function requires that the
#' input directory contains a folder called “pachytene” with the crops in it.
#' @param img_orig original strand crop
#' @param disc_size size of disc for local background calculation in synaptonemal complex channel
#' @param brush_size, size of brush to smooth the foci channel. Should be small
......@@ -419,7 +429,11 @@ get_overlap_mask<- function(strands, foci_label, watershed_stop, img_orig_foci,
#'
#' @param img_file cell's file name
#' @param offset_px, Pixel value offset used in thresholding of synaptonemal complex channel
#' @param stage meitoic stage, currently pachytene or not.
#' @param stage, meiosis stage of interest. Currently count_foci determines
#' this with thresholding/ object properties in the synaptonemal complex channel
#' by previosly calling the get_pachytene function.
#' Note that if using this option, the count_foci function requires that the
#' input directory contains a folder called “pachytene” with the crops in it.
#' @param strands black white mask of strand channel
#' @param watershed_stop Stop default watershed method with "on"
#' @param foci_label black and white mask of foci channel
......@@ -519,10 +533,11 @@ get_C1 <- function(foci_areas, foci_per_cell, C_weigh_foci_number){
#' @param df_cells current data frame
#' @param C_weigh_foci_number choose crispness criteria- defaults to TRUE to use
#' C1 (weighing with number). Otherwise set to FALSE to use C2
#'
#' @param stage, meiosis stage of interest. Currently count_foci determines
#' this with thresholding/ object properties in the synaptonemal complex channel. But will be
#' classified using ML model in future versions.
#' this with thresholding/ object properties in the synaptonemal complex channel
#' by previosly calling the get_pachytene function.
#' Note that if using this option, the count_foci function requires that the
#' input directory contains a folder called “pachytene” with the crops in it.
#' @param offset_px, Pixel value offset used in thresholding of synaptonemal complex channel
#' @param offset_factor, Pixel value offset used in thresholding of foci channel
#' @param brush_size, size of brush to smooth the foci channel. Should be small
......
......@@ -43,7 +43,11 @@ Defaults to -/-.}
\item{cell_count}{unique cell counter}
\item{stage}{meiotic stage}
\item{stage, }{meiosis stage of interest. Currently count_foci determines
this with thresholding/ object properties in the synaptonemal complex channel
by previosly calling the get_pachytene function.
Note that if using this option, the count_foci function requires that the
input directory contains a folder called “pachytene” with the crops in it.}
\item{foci_per_cell}{foci count for cell}
......
......@@ -39,8 +39,10 @@ count_foci(
\item{img_path, }{path containing crops to analyse}
\item{stage, }{meiosis stage of interest. Currently count_foci determines
this with thresholding/ object properties in the synaptonemal complex channel. But will be
classified using ML model in future versions.}
this with thresholding/ object properties in the synaptonemal complex channel
by previosly calling the get_pachytene function.
Note that if using this option, the count_foci function requires that the
input directory contains a folder called “pachytene” with the crops in it.}
\item{offset_px, }{Pixel value offset used in thresholding of synaptonemal complex channel}
......
......@@ -75,8 +75,10 @@ have foci > 100 or so.}
\item{img_orig_foci}{cropped foci channel}
\item{stage, }{meiosis stage of interest. Currently count_foci determines
this with thresholding/ object properties in the synaptonemal complex channel. But will be
classified using ML model in future versions.}
this with thresholding/ object properties in the synaptonemal complex channel
by previosly calling the get_pachytene function.
Note that if using this option, the count_foci function requires that the
input directory contains a folder called “pachytene” with the crops in it.}
\item{WT_str}{string in filename corresponding to wildtype genotype.
Defaults to ++.}
......
......@@ -24,7 +24,11 @@ get_foci_per_cell(
\item{offset_px, }{Pixel value offset used in thresholding of synaptonemal complex channel}
\item{stage}{meitoic stage, currently pachytene or not.}
\item{stage, }{meiosis stage of interest. Currently count_foci determines
this with thresholding/ object properties in the synaptonemal complex channel
by previosly calling the get_pachytene function.
Note that if using this option, the count_foci function requires that the
input directory contains a folder called “pachytene” with the crops in it.}
\item{strands}{black white mask of strand channel}
......
......@@ -16,7 +16,11 @@ make_strand_mask(
\arguments{
\item{offset_px, }{Pixel value offset used in thresholding of synaptonemal complex channel}
\item{stage}{meitoic stage, currently pachytene or not.}
\item{stage, }{meiosis stage of interest. Currently count_foci determines
this with thresholding/ object properties in the synaptonemal complex channel
by previosly calling the get_pachytene function.
Note that if using this option, the count_foci function requires that the
input directory contains a folder called “pachytene” with the crops in it.}
\item{img_orig}{original strand crop}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment