Commit 539a96f5 authored by Lucy McNeill's avatar Lucy McNeill
Browse files

update man files

parent ddbdc9e7
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......@@ -25,7 +25,11 @@ get_distances_along(
annotation,
cell_count,
uid_strand,
per_strand_object
per_strand_object,
KO_str,
WT_str,
KO_out,
WT_out
)
}
\arguments{
......@@ -70,6 +74,14 @@ get_distances_along(
\item{uid_strand}{Unique strand number}
\item{per_strand_object}{Foci per strand object}
\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{
List of fractional distances between foci for all SCs with two. Optional: total distances of SCs. Optional: images of all resulting traces/ foci locations.
......
......@@ -21,7 +21,10 @@ measure_distances(
KO_str = "--",
WT_str = "++",
KO_out = "-/-",
WT_out = "+/+"
WT_out = "+/+",
watershed_stop = "off",
watershed_radius = 1,
watershed_tol = 0.05
)
}
\arguments{
......@@ -58,6 +61,12 @@ measure_distances(
\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
......
......@@ -4,7 +4,7 @@
\alias{threshold_foci_crop}
\title{threshold_foci_crop}
\usage{
threshold_foci_crop(image, offset_factor, brush_size, brush_sigma)
threshold_foci_crop(image, offset_factor, brush_size, brush_sigma, stage)
}
\arguments{
\item{image}{foci channel image}
......@@ -14,6 +14,8 @@ threshold_foci_crop(image, offset_factor, brush_size, brush_sigma)
\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{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.}
}
\value{
A black white mask with foci as objects
......
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