Description Usage Arguments Value Examples
Inner loop of neighborful algorithm used by its variations D and H
1 2 | variation4(colony, combin_coords, neighbors_selected_colony, excluded_colonies,
colony_area_raw_data, plate_median_threshold, param1_threshold)
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colony |
selected colony by the outer loop of the neighborful algorithm |
combin_coords |
combinations of neighbors adjoining the selected colony |
neighbors_selected_colony |
neighbors adjoining the selected colony |
excluded_colonies |
A numeric vector of indices that are part of excluded colonies |
colony_area_raw_data |
A numeric vector of raw data representing the area yeast grown at a specific location on a nutrient medium agar plate |
plate_median_threshold |
This threshold value is computed by multiplying
the value of |
param1_threshold |
The numeric value which can be one from |
A vector of excluded colonies by variation4
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | plateformat <- 1536
middle_colony <- 34
param1_threshold <- 6
neighbors_selected_colony <- middle_neighbors(plateformat, middle_colony)
combin_coords <- combn(length(neighbors_selected_colony), param1_threshold)
data_area <- simulated_data_1536(data_384 = colonyarea$data_subtypes,
in_data_flow = "across",
out_data_flow = "down",
is_plate_coords = TRUE)
empty_indices <- which(convert_small_to_large(plate_from = 384,
plate_to = plateformat,
data_from = colonyarea$data_subtypes,
in_data_flow = 'across',
out_data_flow = "down",
is_plate_coords = FALSE)$y %in% 'Empty')
p_median <- plate_median(empty_indices = empty_indices,
colony_area_raw_data = data_area$y)
plate_median_threshold <- p_median/4
variation4(colony = middle_colony,
combin_coords = combin_coords,
neighbors_selected_colony = neighbors_selected_colony,
excluded_colonies = c(2),
colony_area_raw_data = data_area$y,
plate_median_threshold = plate_median_threshold,
param1_threshold = param1_threshold)
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