update NAMESPACE, DESCRIPTION, man files

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: What the Package Does (Title Case)
 Version: 0.1.0
 Author: Lucy McNeill
-Maintainer: The package maintainer <yourself@somewhere.net>
+Maintainer: The package maintainer <lucmcneill@gmail.com>
 Description: More about what it does (maybe more than one line)
     Use four spaces when indenting paragraphs within the Description.
 Imports: EBImage, stats, utils, graphics

man/auto_crop_fast.Rd

@@ -16,7 +16,12 @@ auto_crop_fast(
   final_blob_amp = 10,
   test_amount = 0,
   brush_size_blob = 51,
-  sigma_blob = 15
+  sigma_blob = 15,
+  channel3_string = "DAPI",
+  channel2_string = "SYCP3",
+  channel1_string = "MLH3",
+  file_ext = "jpeg",
+  third_channel = "off"
 )
 }
 \arguments{

man/count_foci.Rd

@@ -12,7 +12,10 @@ count_foci(
   brush_size = 3,
   brush_sigma = 3,
   foci_norm = 0.01,
-  annotation = "off"
+  annotation = "off",
+  channel2_string = "SYCP3",
+  channel1_string = "MLH3",
+  file_ext = "jpeg"
 )
 }
 \arguments{

man/crop_single_object_fast.Rd

@@ -10,10 +10,10 @@ crop_single_object_fast(
   counter_final,
   img_orig,
   img_orig_foci,
-  img_orig_DAPI,
+  img_orig_DAPI = "blank",
   file_dna,
   file_foci,
-  file_DAPI,
+  file_DAPI = "blank",
   cell_count,
   mean_pix,
   annotation,
@@ -21,7 +21,12 @@ crop_single_object_fast(
   img_path,
   r_max,
   cx,
-  cy
+  cy,
+  channel3_string,
+  channel2_string,
+  channel1_string,
+  file_ext,
+  third_channel
 )
 }
 \arguments{

man/get_pachytene.Rd

@@ -10,7 +10,10 @@ get_pachytene(
   offset = 0.2,
   ecc_thresh = 0.85,
   area_thresh = 0.06,
-  annotation = "off"
+  annotation = "off",
+  channel2_string = "SYCP3",
+  channel1_string = "MLH3",
+  file_ext = "jpeg"
 )
 }
 \arguments{

man/measure_distances.Rd

@@ -14,7 +14,10 @@ measure_distances(
   annotation = "off",
   stage = "pachytene",
   eccentricity_min = 0.6,
-  max_strand_area = 300
+  max_strand_area = 300,
+  channel2_string = "SYCP3",
+  channel1_string = "MLH3",
+  file_ext = "jpeg"
 )
 }
 \arguments{