annotate functions their own helper functions. Amplification factors for RGB output

R/count_foci.R

@@ -44,7 +44,8 @@
 #' @param watershed_tol Intensity tolerance for watershed method. Defaults to 0.05.
 #' @param crowded_foci TRUE or FALSE, defaults to FALSE. Set to TRUE if you
 #' have foci > 100 or so.
-#' @param artificial_amp_factor For annotation only.
+#' @param artificial_amp_factor Amplification of foci channel, for annotation only.
+#' @param strand_amp multiplication of strand channel to make masks
 #' @examples demo_path = paste0(system.file("extdata",package = "synapsis"))
 #' foci_counts <- count_foci(demo_path,offset_factor = 3, brush_size = 3,
 #' brush_sigma = 3, annotation = "on",stage = "pachytene")
@@ -52,7 +53,7 @@
 #' @return foci count per cell
 
 
-count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor = 2, brush_size = 3, brush_sigma = 3, foci_norm = 0.01, annotation = "off",channel2_string = "SYCP3", channel1_string = "MLH3",file_ext = "jpeg", KO_str = "--",WT_str = "++",KO_out = "-/-", WT_out = "+/+", watershed_stop = "off", watershed_radius = 1, watershed_tol = 0.05, crowded_foci = TRUE, artificial_amp_factor = 1)
+count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor = 2, brush_size = 3, brush_sigma = 3, foci_norm = 0.01, annotation = "off",channel2_string = "SYCP3", channel1_string = "MLH3",file_ext = "jpeg", KO_str = "--",WT_str = "++",KO_out = "-/-", WT_out = "+/+", watershed_stop = "off", watershed_radius = 1, watershed_tol = 0.05, crowded_foci = TRUE, artificial_amp_factor = 1, strand_amp = 2)
 {
   cell_count <- 0
   image_count <-0
@@ -82,7 +83,7 @@ count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor
       file_dna <- img_file
       image_count <- image_count +1
       image <- readImage(file_dna)
-      img_orig <- channel(2*image, "grey")
+      img_orig <- channel(strand_amp*image, "grey")
       antibody1_store <- 1
     }
     if(grepl(paste0('*',channel1_string,'.',file_ext,'$'), img_file)){
@@ -142,20 +143,7 @@ count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor
       }
       ### multiply strands by foci_label
       if(annotation == "on"){
-        cat("\n at file",img_file, sep = " ")
-        cat("\n cell counter is", cell_count, sep= " ")
-        cat("\n original images")
-        plot(new_img)
-        plot(img_orig_foci)
-        ch1 <-channel(new_img,"grey")
-        ch2 <- channel(artificial_amp_factor*foci_mask_crop,"grey")
-        bluered <- rgbImage(ch1, ch2, 0*ch1)
-        cat("\n displaying resulting foci count plots. Overlay two channels:")
-        plot(rgbImage(ch1,ch2,0*foci_label))
-        cat("\n coincident foci:")
-        plot(colorLabels(coincident_foci))
-        cat("\n two channels, only coincident foci")
-        plot(rgbImage(strands,coincident_foci,coincident_foci))
+        annotate_foci_counting(img_file,cell_count,new_img,img_orig_foci,artificial_amp_factor,foci_mask_crop,strands,coincident_foci)
       }
       overlap_no <- table(coincident_foci)
       foci_per_cell <-  length(overlap_no)
@@ -218,4 +206,35 @@ count_foci <- function(img_path, stage = "none", offset_px = 0.2, offset_factor
 
 
 
+#' annotate_foci_counting
+#'
+#' Contains all plotting routines for count foci annotation
+#'
+#' @param img_file cell's file name
+#' @param cell_count unique cell counter
+#' @param new_img cropped strand channel
+#' @param img_orig_foci cropped foci channel
+#' @param artificial_amp_factor amplification factor
+#' @param foci_mask_crop black white mask of foci channel
+#' @param strands black white mask of strand channel
+#' @param coincident_foci mask of overlap between strand and foci channel
+#'
+#'
+annotate_foci_counting <- function(img_file,cell_count,new_img,img_orig_foci,artificial_amp_factor,foci_mask_crop,strands,coincident_foci){
+  cat("\n at file",img_file, sep = " ")
+  cat("\n cell counter is", cell_count, sep= " ")
+  cat("\n original images")
+  plot(new_img)
+  plot(img_orig_foci)
+  ch1 <-channel(new_img,"grey")
+  ch2 <- channel(artificial_amp_factor*foci_mask_crop,"grey")
+  bluered <- rgbImage(ch1, ch2, 0*ch1)
+  cat("\n displaying resulting foci count plots. Overlay two channels:")
+  plot(rgbImage(ch1,ch2,0*new_img))
+  cat("\n coincident foci:")
+  plot(colorLabels(coincident_foci))
+  cat("\n two channels, only coincident foci")
+  plot(rgbImage(strands,coincident_foci,coincident_foci))
+}
+
 

R/get_pachytene.R

@@ -26,6 +26,8 @@
 #' @param WT_str string in filename corresponding to wildtype genotype. Defaults to ++.
 #' @param KO_out string in output csv in genotype column, for knockout. Defaults to -/-.
 #' @param WT_out string in output csv in genotype column, for knockout. Defaults to +/+.
+#' @param artificial_amp_factor Amplification of foci channel, for RGB output files. Deaults to 3.
+#' @param strand_amp multiplication of strand channel.
 #' @examples demo_path = paste0(system.file("extdata",package = "synapsis"))
 #' SYCP3_stats <- get_pachytene(demo_path,ecc_thresh = 0.8, area_thresh = 0.04, annotation = "on")
 #' @author Lucy McNeill
@@ -33,7 +35,7 @@
 #'
 
 
-get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh = 0.85, area_thresh = 0.06, annotation = "off", channel2_string = "SYCP3", channel1_string = "MLH3",file_ext = "jpeg", KO_str = "--",WT_str = "++",KO_out = "-/-", WT_out = "+/+", path_out = img_path)
+get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh = 0.85, area_thresh = 0.06, annotation = "off", channel2_string = "SYCP3", channel1_string = "MLH3",file_ext = "jpeg", KO_str = "--",WT_str = "++",KO_out = "-/-", WT_out = "+/+", path_out = img_path, artificial_amp_factor=3, strand_amp = 2)
 {
   cell_count <- 0
   image_count <-0
@@ -66,7 +68,7 @@ get_pachytene <- function(img_path, species_num = 20, offset = 0.2,ecc_thresh =
       file_base_dna <- file_base
       image_count <- image_count +1
       image <- readImage(file_dna)
-      img_orig <- channel(image, "grey")
+      img_orig <- channel(strand_amp*image, "grey")
       antibody1_store <- 1
     }
     if(grepl(paste0('*',channel1_string,'.',file_ext,'$'), img_file)){

man/annotate_foci_counting.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/count_foci.R
+\name{annotate_foci_counting}
+\alias{annotate_foci_counting}
+\title{annotate_foci_counting}
+\usage{
+annotate_foci_counting(
+  img_file,
+  cell_count,
+  new_img,
+  img_orig_foci,
+  artificial_amp_factor,
+  foci_mask_crop,
+  strands,
+  coincident_foci
+)
+}
+\arguments{
+\item{img_file}{cell's file name}
+
+\item{cell_count}{unique cell counter}
+
+\item{new_img}{cropped strand channel}
+
+\item{img_orig_foci}{cropped foci channel}
+
+\item{artificial_amp_factor}{amplification factor}
+
+\item{foci_mask_crop}{black white mask of foci channel}
+
+\item{strands}{black white mask of strand channel}
+
+\item{coincident_foci}{mask of overlap between strand and foci channel}
+}
+\description{
+Contains all plotting routines for count foci annotation
+}

man/count_foci.Rd

@@ -24,7 +24,8 @@ count_foci(
   watershed_radius = 1,
   watershed_tol = 0.05,
   crowded_foci = TRUE,
-  artificial_amp_factor = 1
+  artificial_amp_factor = 1,
+  strand_amp = 2
 )
 }
 \arguments{
@@ -78,7 +79,9 @@ in foci channel. Defaults to 1 (small)}
 \item{crowded_foci}{TRUE or FALSE, defaults to FALSE. Set to TRUE if you
 have foci > 100 or so.}
 
-\item{artificial_amp_factor}{For annotation only.}
+\item{artificial_amp_factor}{Amplification of foci channel, for annotation only.}
+
+\item{strand_amp}{multiplication of strand channel to make masks}
 }
 \value{
 foci count per cell

man/get_pachytene.Rd

@@ -18,7 +18,9 @@ get_pachytene(
   WT_str = "++",
   KO_out = "-/-",
   WT_out = "+/+",
-  path_out = img_path
+  path_out = img_path,
+  artificial_amp_factor = 3,
+  strand_amp = 2
 )
 }
 \arguments{
@@ -49,6 +51,10 @@ get_pachytene(
 \item{WT_out}{string in output csv in genotype column, for knockout. Defaults to +/+.}
 
 \item{path_out, }{user specified output path. Defaults to img_path}
+
+\item{artificial_amp_factor}{Amplification of foci channel, for RGB output files. Deaults to 3.}
+
+\item{strand_amp}{multiplication of strand channel.}
 }
 \value{
 Pairs of foci and SC channel crops for pachytene