Commit 3f75ab8c authored by Lucy McNeill's avatar Lucy McNeill
Browse files

update NAMESPACE, DESCRIPTION, man files

parent 6e867187
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......@@ -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
......
......@@ -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{
......
......@@ -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{
......
......@@ -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{
......
......@@ -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{
......
......@@ -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{
......
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