Commit b0be1acd authored by Lucy McNeill's avatar Lucy McNeill
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coint_foci has option minimum foci

parent 3422fd64
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...@@ -54,7 +54,7 @@ ...@@ -54,7 +54,7 @@
#' @return foci count per cell #' @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, strand_amp = 2, min_foci =9) 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, min_foci =1)
{ {
cell_count <- 0 cell_count <- 0
image_count <-0 image_count <-0
......
...@@ -26,7 +26,7 @@ count_foci( ...@@ -26,7 +26,7 @@ count_foci(
crowded_foci = TRUE, crowded_foci = TRUE,
artificial_amp_factor = 1, artificial_amp_factor = 1,
strand_amp = 2, strand_amp = 2,
min_foci = 9 min_foci = 1
) )
} }
\arguments{ \arguments{
......
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