coint_foci has option minimum foci

R/count_foci.R

@@ -54,7 +54,7 @@
 #' @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, 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
   image_count <-0

man/count_foci.Rd

@@ -26,7 +26,7 @@ count_foci(
   crowded_foci = TRUE,
   artificial_amp_factor = 1,
   strand_amp = 2,
-  min_foci = 9
+  min_foci = 1
 )
 }
 \arguments{