only remaining CMD check warning relates to libraries. No undefined variables anymore

DESCRIPTION

@@ -2,11 +2,11 @@ Package: synapsis
 Type: Package
 Title: What the Package Does (Title Case)
 Version: 0.1.0
-Author: Who wrote it
+Author: Lucy McNeill
 Maintainer: The package maintainer <yourself@somewhere.net>
 Description: More about what it does (maybe more than one line)
     Use four spaces when indenting paragraphs within the Description.
-License: What license is it under?
+License: GPL (>=3)
 Encoding: UTF-8
 LazyData: true
 Imports: 
@@ -15,3 +15,6 @@ Imports:
     graphics,
     utils
 RoxygenNote: 7.1.1
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

R/auto_crop.R

@@ -7,8 +7,17 @@
 #' @import graphics
 #' @import utils
 #' @export auto_crop
-#' @param file_list The file list
-#' @param img_path The path
+#' @param img_path, The path
+#' @param max_cell_area, description
+#' @param min_cell_area, description
+#' @param mean_pix, description
+#' @param annotation, description
+#' @param blob_factor, description
+#' @param bg_blob_factor, description
+#' @param offset, description
+#' @param final_blob_amp, description
+#' @param test_amount, description
+
 #' @return cropped SC and foci channels around single cells, regardless of stage
 
 
@@ -33,7 +42,6 @@ auto_crop <- function(img_path,  max_cell_area = 20000, min_cell_area = 7000, me
     print(file)
     file_base = file
     filename_path_test = paste0(img_path,"/", file)
-    print(filename_path_test)
     file = filename_path_test
     if(grepl("*DAPI.jpeg$", file)){
       file_DAPI = file
@@ -121,6 +129,11 @@ print("viable cells")
 #' @import EBImage
 #' @export
 #' @param img_orig Original image
+#' @param blob_factor, description
+#' @param bg_blob_factor, description
+#' @param offset, description
+#' @param final_blob_amp, description
+
 #' @return Mask with cell candidates
 
 #################################### new function ####################################
@@ -161,16 +174,12 @@ get_blobs <- function(img_orig, blob_factor, bg_blob_factor, offset,final_blob_a
 #' @import EBImage
 #' @export
 #' @param candidate Mask of individual cell candidates
+#' @param max_cell_area, description
+#' @param min_cell_area, description
+
 #' @return Mask of cell candidates which meet size criteria
 keep_cells <- function(candidate, max_cell_area, min_cell_area){
 
-
-  # input:
-
-  # output:
-
-
-
   # delete everything that's too small
   colorimg<- colorLabels(candidate, normalize = TRUE)
   x <- computeFeatures.shape(candidate)
@@ -208,6 +217,24 @@ keep_cells <- function(candidate, max_cell_area, min_cell_area){
 #' @import EBImage
 #' @export
 #' @param retained Mask of cell candidates which meet size criteria
+#' @param OOI_final, description
+#' @param counter_final, description
+#' @param img_orig, description
+#' @param img_orig_foci, description
+#' @param img_orig_DAPI, description
+#' @param file_dna, description
+#' @param file_foci, description
+#' @param file_DAPI, description
+#' @param cell_count, description
+#' @param mean_pix, description
+#' @param annotation, description
+#' @param file_base, description
+#' @param img_path, description
+
+#'
+
+
+
 #' @return Crops aroudn all candidates in both channels
 #'
 crop_single_object <- function(retained, OOI_final,counter_final,img_orig,img_orig_foci,img_orig_DAPI,file_dna,file_foci,file_DAPI,cell_count, mean_pix, annotation, file_base, img_path){
@@ -242,9 +269,8 @@ crop_single_object <- function(retained, OOI_final,counter_final,img_orig,img_or
   # I think this is quick enough for now.. takes less than 10s...
   xx = data.frame(as.numeric(tmp_img))
   xx <- data.frame(bwlabel(tmp_img))
-  xm2 = t(as.matrix(xx))
+  my_matrix = t(as.matrix(xx))
   i <- 0
-  my_matrix <- xm2
   ### now loop over matrix
   for(row in 1:nrow(my_matrix)) {
     for(col in 1:ncol(my_matrix)) {

R/count_foci.R

@@ -7,7 +7,15 @@
 #' @import graphics
 #' @import utils
 #' @export count_foci
-#' @param file_list list of files
+#' @param img_path, path of crops
+#' @param stage, description
+#' @param offset_px, description
+#' @param offset_factor, description
+#' @param brush_size, description
+#' @param brush_sigma, description
+#' @param foci_norm, description
+#' @param annotate, description
+
 #' @return foci count per cell
 
 

R/get_pachytene.R

@@ -7,8 +7,12 @@
 #' @import graphics
 #' @import utils
 #' @export get_pachytene
-#' @param file_list The file list
 #' @param img_path The path
+#' @param species_num, description
+#' @param offset, description
+#' @param ecc_thresh, description
+#' @param area_thresh, description
+
 #' @return Pairs of foci and SC channel crops for pachytene
 
 

R/measure_distances.R

@@ -4,8 +4,17 @@
 #'
 #' @import EBImage
 #' @export
-#' @param file_list The file list
 #' @param img_path The path
+#' @param offset_px, description
+#' @param offset_factor, description
+#' @param brush_size, description
+#' @param brush_sigma, description
+#' @param foci_norm, description
+#' @param annotate, description
+#' @param offset_SC, description
+#' @param stage, description
+#' @param eccentricity_min, description
+#' @param max_strand_area, description
 #' @return Histogram of distances
 
 # should take in same values as count_foci..
@@ -192,7 +201,9 @@ threshold_SC_crop <- function(image, offset){
 #' Creates mask for foci channel
 #'
 #' @param image foci channel image
-#' @param offset offset for a foci signal
+#' @param offset_factor offset for a foci signal
+#' @param brush_size, description
+#' @param brush_sigma, description
 #' @return A black white mask with foci as objects
 #'
 threshold_foci_crop <- function(image, offset_factor, brush_size, brush_sigma){
@@ -222,14 +233,18 @@ threshold_foci_crop <- function(image, offset_factor, brush_size, brush_sigma){
 #'
 #' Creates mask for SC channel
 #'
-#' @param strands A black white mask with SCs as objects
-#' @param num_strands offset for an SC signal
-#' @param new_img hello
-#' @param foci_label A black white mask with foci as objects
-#' @param dimensionless_dist hello
-#' @param SC_lengths hello
-#' @param foci_count_strand hello
-#' @param strand_iter hello
+#' @param strands, A black white mask with SCs as objects
+#' @param num_strands, description
+#' @param new_img, description
+#' @param foci_label, A black white mask with foci as objects
+#' @param SC_lengths, description
+#' @param foci_count_strand, description
+#' @param strand_iter, description
+#' @param file, description
+#' @param annotate, description
+#' @param eccentricity_min, description
+#' @param max_strand_area, description
+
 #' @return A list of distances
 #'
 get_distance <- function(strands,num_strands,new_img,foci_label, SC_lengths, foci_count_strand, strand_iter,file,annotate, eccentricity_min, max_strand_area){
@@ -513,6 +528,12 @@ get_first_dir <- function(noise_gone,ix,iy,window){
 #' Moves one pixel away from the starting point
 #'
 #' @param chosen_dir The brightest direction of a line passing through starting point
+#' @param ix1, description
+#' @param ix2, description
+#' @param iy1, description
+#' @param iy2, description
+#' @param distance_strand, description
+#' @param distance_strand_2, description
 #' @return New sub square for first and second branch
 
 first_shot_out <- function(chosen_dir, ix1,ix2,iy1,iy2,distance_strand, distance_strand_2){
@@ -585,7 +606,15 @@ first_shot_out <- function(chosen_dir, ix1,ix2,iy1,iy2,distance_strand, distance
 #'
 #' Moves one pixel away one first branch
 #'
+
+#' @param new_square_1, description
+#' @param ix1, description
+#' @param iy1, description
+#' @param dir_1, description
+#' @param window, description
 #' @param chosen_dir The brightest direction of the previous step
+#' @param distance_strand, description
+#' @param first_dir, description
 #' @return New sub square for first branch after taking one step
 #'
 get_next_first_dir <- function(new_square_1,ix1,iy1,dir_1,window,chosen_dir,distance_strand,first_dir){
@@ -910,11 +939,21 @@ get_next_first_dir <- function(new_square_1,ix1,iy1,dir_1,window,chosen_dir,dist
 
 
 
+
 #' get_next_second_dir
 #'
 #' Moves one pixel away one second branch. Terminates if at the end of the SC.
 #'
+
+#' @param new_square_2, description
+#' @param ix2, description
+#' @param iy2, description
+#' @param dir_2, description
+#' @param window, description
 #' @param chosen_dir The brightest direction of the previous step
+#' @param distance_strand_2, description
+#' @param second_dir, description
+
 #' @return New sub square for second branch after taking one step
 #'
 
@@ -1190,7 +1229,24 @@ get_next_second_dir <- function(new_square_2,ix2,iy2,dir_2,window,chosen_dir,dis
 #'
 #' Calculates the pixel distance
 #'
-#' @param chosen_dir The brightest direction of the previous step
+#' @param distance_strand, description
+#' @param distance_strand_2, description
+#' @param per_strand, description
+#' @param foci_label, description
+#' @param walkers, description
+#' @param noise_gone, description
+#' @param start_x, description
+#' @param start_y, description
+#' @param start_x2, description
+#' @param start_y2, description
+#' @param start_dir, description
+#' @param cx, description
+#' @param cy, description
+#' @param mean_x, description
+#' @param mean_y, description
+#' @param strand_iter, description
+#' @param file, description
+#' @param annotate, description
 #' @return List of fractional distances between foci for all SCs with two. Optional: total distances of SCs. Optional: images of all resulting traces/ foci locations.
 #'
 get_distance_between_two <- function(distance_strand,distance_strand_2,per_strand,foci_label, walkers, noise_gone,start_x,start_y,start_x2,start_y2,start_dir,cx,cy,mean_x,mean_y,strand_iter,file,annotate){

man/auto_crop.Rd

@@ -6,16 +6,37 @@
 \usage{
 auto_crop(
   img_path,
-  crop_method = "regular",
   max_cell_area = 20000,
   min_cell_area = 7000,
-  mean_pix = 0.08
+  mean_pix = 0.08,
+  annotation = "off",
+  blob_factor = 15,
+  bg_blob_factor = 10,
+  offset = 0.2,
+  final_blob_amp = 10,
+  test_amount = 0
 )
 }
 \arguments{
-\item{img_path}{The path}
+\item{img_path, }{The path}
 
-\item{file_list}{The file list}
+\item{max_cell_area, }{description}
+
+\item{min_cell_area, }{description}
+
+\item{mean_pix, }{description}
+
+\item{annotation, }{description}
+
+\item{blob_factor, }{description}
+
+\item{bg_blob_factor, }{description}
+
+\item{offset, }{description}
+
+\item{final_blob_amp, }{description}
+
+\item{test_amount, }{description}
 }
 \value{
 cropped SC and foci channels around single cells, regardless of stage

man/count_foci.Rd

@@ -16,7 +16,21 @@ count_foci(
 )
 }
 \arguments{
-\item{file_list}{list of files}
+\item{img_path, }{path of crops}
+
+\item{stage, }{description}
+
+\item{offset_px, }{description}
+
+\item{offset_factor, }{description}
+
+\item{brush_size, }{description}
+
+\item{brush_sigma, }{description}
+
+\item{foci_norm, }{description}
+
+\item{annotate, }{description}
 }
 \value{
 foci count per cell

man/crop_single_object.Rd

@@ -15,11 +15,40 @@ crop_single_object(
   file_foci,
   file_DAPI,
   cell_count,
-  mean_pix
+  mean_pix,
+  annotation,
+  file_base,
+  img_path
 )
 }
 \arguments{
 \item{retained}{Mask of cell candidates which meet size criteria}
+
+\item{OOI_final, }{description}
+
+\item{counter_final, }{description}
+
+\item{img_orig, }{description}
+
+\item{img_orig_foci, }{description}
+
+\item{img_orig_DAPI, }{description}
+
+\item{file_dna, }{description}
+
+\item{file_foci, }{description}
+
+\item{file_DAPI, }{description}
+
+\item{cell_count, }{description}
+
+\item{mean_pix, }{description}
+
+\item{annotation, }{description}
+
+\item{file_base, }{description}
+
+\item{img_path, }{description}
 }
 \value{
 Crops aroudn all candidates in both channels

man/first_shot_out.Rd

@@ -16,6 +16,18 @@ first_shot_out(
 }
 \arguments{
 \item{chosen_dir}{The brightest direction of a line passing through starting point}
+
+\item{ix1, }{description}
+
+\item{ix2, }{description}
+
+\item{iy1, }{description}
+
+\item{iy2, }{description}
+
+\item{distance_strand, }{description}
+
+\item{distance_strand_2, }{description}
 }
 \value{
 New sub square for first and second branch

man/get_blobs.Rd

@@ -4,10 +4,18 @@
 \alias{get_blobs}
 \title{get_blobs}
 \usage{
-get_blobs(img_orig, crop_method = "regular")
+get_blobs(img_orig, blob_factor, bg_blob_factor, offset, final_blob_amp)
 }
 \arguments{
 \item{img_orig}{Original image}
+
+\item{blob_factor, }{description}
+
+\item{bg_blob_factor, }{description}
+
+\item{offset, }{description}
+
+\item{final_blob_amp, }{description}
 }
 \value{
 Mask with cell candidates

man/get_distance.Rd

@@ -9,30 +9,37 @@ get_distance(
   num_strands,
   new_img,
   foci_label,
-  dimensionless_dist,
   SC_lengths,
   foci_count_strand,
   strand_iter,
   file,
-  annotate
+  annotate,
+  eccentricity_min,
+  max_strand_area
 )
 }
 \arguments{
-\item{strands}{A black white mask with SCs as objects}
+\item{strands, }{A black white mask with SCs as objects}
 
-\item{num_strands}{offset for an SC signal}
+\item{num_strands, }{description}
 
-\item{new_img}{hello}
+\item{new_img, }{description}
 
-\item{foci_label}{A black white mask with foci as objects}
+\item{foci_label, }{A black white mask with foci as objects}
 
-\item{dimensionless_dist}{hello}
+\item{SC_lengths, }{description}
 
-\item{SC_lengths}{hello}
+\item{foci_count_strand, }{description}
 
-\item{foci_count_strand}{hello}
+\item{strand_iter, }{description}
 
-\item{strand_iter}{hello}
+\item{file, }{description}
+
+\item{annotate, }{description}
+
+\item{eccentricity_min, }{description}
+
+\item{max_strand_area, }{description}
 }
 \value{
 A list of distances

man/get_distance_between_two.Rd

@@ -21,13 +21,46 @@ get_distance_between_two(
   mean_x,
   mean_y,
   strand_iter,
-  dimensionless_dist,
   file,
   annotate
 )
 }
 \arguments{
-\item{chosen_dir}{The brightest direction of the previous step}
+\item{distance_strand, }{description}
+
+\item{distance_strand_2, }{description}
+
+\item{per_strand, }{description}
+
+\item{foci_label, }{description}
+
+\item{walkers, }{description}
+
+\item{noise_gone, }{description}
+
+\item{start_x, }{description}
+
+\item{start_y, }{description}
+
+\item{start_x2, }{description}
+
+\item{start_y2, }{description}
+
+\item{start_dir, }{description}
+
+\item{cx, }{description}
+
+\item{cy, }{description}
+
+\item{mean_x, }{description}
+
+\item{mean_y, }{description}
+
+\item{strand_iter, }{description}
+
+\item{file, }{description}
+
+\item{annotate, }{description}
 }
 \value{
 List of fractional distances between foci for all SCs with two. Optional: total distances of SCs. Optional: images of all resulting traces/ foci locations.

man/get_next_first_dir.Rd

@@ -16,7 +16,21 @@ get_next_first_dir(
 )
 }
 \arguments{
+\item{new_square_1, }{description}
+
+\item{ix1, }{description}
+
+\item{iy1, }{description}
+
+\item{dir_1, }{description}
+
+\item{window, }{description}
+
 \item{chosen_dir}{The brightest direction of the previous step}
+
+\item{distance_strand, }{description}
+
+\item{first_dir, }{description}
 }
 \value{
 New sub square for first branch after taking one step

man/get_next_second_dir.Rd

@@ -16,7 +16,21 @@ get_next_second_dir(
 )
 }
 \arguments{
+\item{new_square_2, }{description}
+
+\item{ix2, }{description}
+
+\item{iy2, }{description}
+
+\item{dir_2, }{description}
+
+\item{window, }{description}
+
 \item{chosen_dir}{The brightest direction of the previous step}
+
+\item{distance_strand_2, }{description}
+
+\item{second_dir, }{description}
 }
 \value{
 New sub square for second branch after taking one step

man/get_pachytene.Rd

@@ -15,7 +15,13 @@ get_pachytene(
 \arguments{
 \item{img_path}{The path}
 
-\item{file_list}{The file list}
+\item{species_num, }{description}
+
+\item{offset, }{description}
+
+\item{ecc_thresh, }{description}
+
+\item{area_thresh, }{description}
 }
 \value{
 Pairs of foci and SC channel crops for pachytene

man/keep_cells.Rd

@@ -8,6 +8,10 @@ keep_cells(candidate, max_cell_area, min_cell_area)
 }
 \arguments{
 \item{candidate}{Mask of individual cell candidates}
+
+\item{max_cell_area, }{description}
+
+\item{min_cell_area, }{description}
 }
 \value{
 Mask of cell candidates which meet size criteria

man/measure_distances.Rd

@@ -7,19 +7,39 @@
 measure_distances(
   img_path,
   offset_px = 0.2,
-  offset_factor = 2,
+  offset_factor = 3,
   brush_size = 3,
   brush_sigma = 3,
   foci_norm = 0.01,
   annotate = "off",
   offset_SC = 0.2,
-  stage = "pachytene"
+  stage = "pachytene",
+  eccentricity_min = 0.6,
+  max_strand_area = 300
 )
 }
 \arguments{
 \item{img_path}{The path}
 
-\item{file_list}{The file list}
+\item{offset_px, }{description}
+
+\item{offset_factor, }{description}
+
+\item{brush_size, }{description}
+
+\item{brush_sigma, }{description}
+
+\item{foci_norm, }{description}
+
+\item{annotate, }{description}
+
+\item{offset_SC, }{description}
+
+\item{stage, }{description}
+
+\item{eccentricity_min, }{description}
+
+\item{max_strand_area, }{description}
 }
 \value{
 Histogram of distances

man/threshold_foci_crop.Rd

@@ -9,7 +9,11 @@ threshold_foci_crop(image, offset_factor, brush_size, brush_sigma)
 \arguments{
 \item{image}{foci channel image}
 
-\item{offset}{offset for a foci signal}
+\item{offset_factor}{offset for a foci signal}