Commit 4066a293 authored by Lucy McNeill's avatar Lucy McNeill
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measures the distance along for each foci on a strand with 2 or more foci

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/measure_distances_general.R
\name{get_distance_general}
\alias{get_distance_general}
\title{get_distance_general
Creates mask for SC channel}
\usage{
get_distance_general(
strands,
num_strands,
new_img,
foci_label,
foci_count_strand,
strand_iter,
file,
annotation,
eccentricity_min,
max_strand_area,
cell_count,
KO_str,
WT_str,
KO_out,
WT_out
)
}
\arguments{
\item{strands, }{A black white mask with SCs as objects}
\item{num_strands, }{Number of individual strands on SC mask}
\item{new_img, }{Original strand/dna/SYCP3 channel image with noise removed.}
\item{foci_label, }{A black white mask with foci as objects}
\item{foci_count_strand, }{Number of foci counted located on the one SC}
\item{strand_iter, }{Strand number in iteration over all in cell}
\item{file, }{original filename that cell candidate came from. Used to identify e.g. genotype for data frame.}
\item{annotation, }{Choice to output pipeline choices (recommended to knit)}
\item{eccentricity_min, }{The minimum eccentricity (from computefeatures) of a strand to proceed with measuring}
\item{max_strand_area, }{Maximum pixel area of a strand}
\item{cell_count}{Unique cell counter}
\item{KO_str}{string in filename corresponding to knockout genotype. Defaults to --.}
\item{WT_str}{string in filename corresponding to wildtype genotype. Defaults to ++.}
\item{KO_out}{string in output csv in genotype column, for knockout. Defaults to -/-.}
\item{WT_out}{string in output csv in genotype column, for knockout. Defaults to +/+.}
}
\value{
Data frame with properties of synaptonemal (SC) measurements
}
\description{
get_distance_general
Creates mask for SC channel
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/measure_distances_general.R
\name{get_distances_along}
\alias{get_distances_along}
\title{get_distances_along}
\usage{
get_distances_along(
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,
annotation,
cell_count,
uid_strand,
per_strand_object
)
}
\arguments{
\item{distance_strand, }{total distance along first branch}
\item{distance_strand_2, }{total distance along second branch}
\item{per_strand, }{Mask with colocalizing foci}
\item{foci_label, }{black white mask with foci as objects, not necessarily on SC. Needed for computefeatures.}
\item{walkers, }{black white mask containing the line that traces through the middle of the SC. Computed earlier in get_distance}
\item{noise_gone, }{Black white mask with the single SC to be measured}
\item{start_x, }{x pixel location of where first branch terminated}
\item{start_y, }{y pixel location of where first branch terminated}
\item{start_x2, }{x pixel location of where second branch terminated}
\item{start_y2, }{y pixel location of where second branch terminated}
\item{start_dir, }{direction that the first branch was traveling along when it terminated}
\item{cx, }{centre of intensity x of the SC from computefeatures (annotation purposes only)}
\item{cy, }{centre of intensity y of the SC from computefeatures (annotation purposes only)}
\item{mean_x, }{starting point x that the two branches move away from to trace out the SC (annotation purposes only)}
\item{mean_y, }{starting point x that the two branches move away from to trace out the SC (annotation purposes only)}
\item{strand_iter, }{Strand number in iteration over all in cell}
\item{file, }{original filename that cell candidate came from. Used to identify e.g. genotype for data frame.}
\item{annotation, }{Choice to output pipeline choices (recommended to knit)}
\item{cell_count}{Unique cell number}
\item{uid_strand}{Unique strand number}
\item{per_strand_object}{Foci per strand object}
}
\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.
}
\description{
Calculates the pixel distance
}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/measure_distances_general.R
\name{measure_distances_general}
\alias{measure_distances_general}
\title{measure_distances_general}
\usage{
measure_distances_general(
img_path,
offset_px = 0.2,
offset_factor = 3,
brush_size = 3,
brush_sigma = 3,
foci_norm = 0.01,
annotation = "off",
stage = "pachytene",
eccentricity_min = 0.6,
max_strand_area = 300,
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
)
}
\arguments{
\item{img_path, }{path containing image data to analyse}
\item{offset_px, }{Pixel value offset used in thresholding of dna channel}
\item{offset_factor, }{Pixel value offset used in thresholding of foci channel}
\item{brush_size, }{size of brush to smooth the foci channel. Should be small to avoid erasing foci.}
\item{brush_sigma, }{sigma for Gaussian smooth of foci channel. Should be small to avoid erasing foci.}
\item{foci_norm, }{Mean intensity to normalise all foci channels to.}
\item{annotation, }{Choice to output pipeline choices (recommended to knit)}
\item{stage, }{meiosis stage of interest. Currently count_foci determines this with thresholding/ object properties in the dna channel. But will be classified using ML model in future versions.}
\item{eccentricity_min, }{The minimum eccentricity (from computefeatures) of a strand to proceed with measuring}
\item{max_strand_area, }{Maximum pixel area of a strand}
\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. tiff jpeg or png.}
\item{KO_str}{string in filename corresponding to knockout genotype. Defaults to --.}
\item{WT_str}{string in filename corresponding to wildtype genotype. Defaults to ++.}
\item{KO_out}{string in output csv in genotype column, for knockout. Defaults to -/-.}
\item{WT_out}{string in output csv in genotype column, for knockout. Defaults to +/+.}
\item{watershed_stop}{Turn off default watershed method with "off"}
\item{watershed_radius}{Radius (ext variable) in watershed method used in foci channel. Defaults to 1 (small)}
\item{watershed_tol}{Intensity tolerance for watershed method. Defaults to 0.05.}
}
\value{
Data frame with properties of synaptonemal (SC) measurements
}
\description{
Measure the distance between foci on a synaptonemal complex
}
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