get_coincident_foci {synapsis} | R Documentation |
calculates the statistic to compare to crisp_criteria, which determines whether the foci count will be reliable
get_coincident_foci( offset_px, offset_factor, brush_size, brush_sigma, annotation, watershed_stop, watershed_radius, watershed_tol, crowded_foci, artificial_amp_factor, strand_amp, disc_size, disc_size_foci, img_file, cell_count, img_orig, img_orig_foci, stage, WT_str, KO_str, WT_out, KO_out, C1_search, discrepant_category, C1, C2, df_cells, C_weigh_foci_number )
offset_px, |
Pixel value offset used in thresholding of synaptonemal complex channel |
offset_factor, |
Pixel value offset used in thresholding of foci channel |
brush_size, |
size of brush to smooth the foci channel. Should be small to avoid erasing foci. |
brush_sigma, |
sigma for Gaussian smooth of foci channel. Should be small to avoid erasing foci. |
annotation, |
Choice to output pipeline choices (recommended to knit) |
watershed_stop |
Stop default watershed method with "on" |
watershed_radius |
Radius (ext variable) in watershed method used in foci channel. Defaults to 1 (small) |
watershed_tol |
Intensity tolerance for watershed method. Defaults to 0.05. |
crowded_foci |
TRUE or FALSE, defaults to FALSE. Set to TRUE if you have foci > 100 or so. |
artificial_amp_factor |
Amplification of foci channel, for annotation only. |
strand_amp |
multiplication of strand channel to make masks |
disc_size |
size of disc for local background calculation in synaptonemal complex channel |
disc_size_foci |
size of disc for local background calculation in foci channel |
img_file |
cell's file name |
cell_count |
unique cell counter |
img_orig |
original strand crop |
img_orig_foci |
cropped foci channel |
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. |
WT_str |
string in filename corresponding to wildtype genotype. Defaults to ++. |
KO_str |
string in filename corresponding to knockout genotype. Defaults to –. |
WT_out |
string in output csv in genotype column, for knockout. Defaults to +/+. |
KO_out |
string in output csv in genotype column, for knockout. Defaults to -/-. |
C1_search |
TRUE or FALSE whether the image is still being modified until it meets the crispness criteria |
discrepant_category |
estimated number of foci that are NOT on a strand. |
C1 |
Default crispness criteria = sd(foci_area)/(mean(foci_area)+1) |
C2 |
Alternative crisp criteria. |
df_cells |
current data frame |
C_weigh_foci_number |
choose crispness criteria- defaults to TRUE to use C1 (weighing with number). Otherwise set to FALSE to use C2 |
data frame with new row with most recent foci per cell appended