excluded_coloniesE: Neighborful algorithm - Variation-E

In sathishsrinivasank/pinerrordetector: Detection of Pinning Errors of Robotic Machines used in SGA Yeast Screen

Description

The variation-E of neighborful algorithm uses both param1_threshold and param2_threshold exclusion criteria to remove colonies as excluded ones by removing empty_indices from both outer and inner loops of the algorithm. The outer loop of the algorithm is used to iterate over the list of colony indices. The inner loop of the algorithm is used to iterate over all possible combinations of adjoining neighbors of a selected colony from the outer loop.

Usage

excluded_coloniesE(plateformat, colony_indices, colony_area_raw_data,
  empty_indices, excluded_colonies, plate_median_threshold, param1_threshold,
  param2_threshold, is_middle)

Arguments

plateformat	An integer which can be one of 96 or 384 or 1536
colony_indices	A vector of indices. If the value of is_middle is TRUE, then middle colony indices must be used. If the value of is_middle is FALSE, then peripheral colony indices must be used
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
empty_indices	A numeric vector of indexed empty locations. It can also be the indices of control colonies grown on a plate, which may be used for normalizing the colony area of a plate
excluded_colonies	A numeric vector of indices that are part of excluded colonies
plate_median_threshold	This threshold value is computed by multiplying the value of percent_median_thresh with the value from plate_median(empty_indices,colony_area_raw_data) and dividing it by 100
param1_threshold	The numeric value which can be one from 1:8. This exclusion criteria-1 of neighborful algorithm represents the number of adjoining neighbors of the selected colony from colony_indices that has colony area less than or equal to plate_median_threshold. If the selected colony is surrounded by at least param1_threshold neighbors, then it will be considered as excluded colony by the neighborful algorithm
param2_threshold	The numeric value which can be one from 1:8. This exclusion criteria-2 of neighborful algorithm represents the number of adjoing neighbors of the selected colony from colony_indices are excluded by the previous iteration of neighborful algorithm of variation-E. If the selected colony is surrounded by at least param2_threshold neighbors, then it will be considered as excluded colony by the neighborful algorithm
is_middle	logical. If TRUE, then colony_indices must have indices from the middle of the plate. If FALSE, then colony_indices must have indices from the periphery of the plate

Value

The numeric vector of excluded colonies by neighborful algorithm of variation-E

Examples

plateformat <- 1536
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
all_indices <- 1:plateformat
middle_colony_indices <- all_indices[-(not_middle_indices(plateformat))]
excluded_coloniesE(plateformat = plateformat,
                   colony_indices = middle_colony_indices,
                   colony_area_raw_data = data_area$y,
                   empty_indices = empty_indices,
                   excluded_colonies = c(),
                   plate_median_threshold = plate_median_threshold,
                   param1_threshold = 1,
                   param2_threshold = 1,
                   is_middle = TRUE)

sathishsrinivasank/pinerrordetector documentation built on May 7, 2019, 2:55 a.m.