## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(frenchFISH) set.seed(366) ## ----readin_autocounts-------------------------------------------------------- fishalyserCsvPath <- system.file("extdata", "SampleFISH.jpg_data.csv", package="frenchFISH") automatic_counts <- convertFishalyserCsvToCountMatrix(fishalyserCsvPath) ## ----correct_autocounts------------------------------------------------------- set.seed(366) nuclear_radius <- 40 section_height <- 5 corrected_automatic_counts <- getAutomaticCountsEstimates(automatic_counts, nuclear_radius, section_height) ## ----print_corrected_autocounts----------------------------------------------- print(corrected_automatic_counts) ## ----readin_manualcounts------------------------------------------------------ manual_counts <- cbind(red = round(runif(20,0,5), 0), green = round(runif(20,0,5), 0), blue = round(runif(20,0,5), 0)) ## ----correct_manualcounts----------------------------------------------------- nuclear_radius <- 8 section_height <- 4 corrected_manual_counts <- getManualCountsEstimates(manual_counts, nuclear_radius, section_height) ## ----print_corrected_manualcounts--------------------------------------------- print(corrected_manual_counts)