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| Package: LEEF.2.measurement.flowcytometer | ||
| Type: Package | ||
| Title: What the Package Does (Title Case) | ||
| Version: 0.9.5 | ||
| Version: 0.9.7 | ||
| Authors@R: c( | ||
| person(given = "Rainer M.", family = "Krug", email = "[email protected]", role = c("aut", "cre")), | ||
| person("SNF Project 310030_188431", role = "fnd") | ||
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| #' Extract flowcytometer traits | ||
| #' | ||
| #' NOT USED IN PIPLELINE!!!! | ||
| #' This function is extracting data to be added to the database | ||
| #' (and therefore make accessible for further analysis and forecasting) | ||
| #' from \code{.fcs} files. | ||
| #' | ||
| #' @param input directory from which to read the data | ||
| #' @param metadata_flowcytometer the content of the file | ||
| #' \code{metadata_flowcytometer.csv} which will be linked into the traits | ||
| #' @param min_FSC.A numeric. If \code{!NULL}, \code{FSA.A <= min_FSC.A} will be fitered out by using | ||
| #' a rectangular filter | ||
| #' \code{flowCore::rectangleGate(filterId="filter_out_0", "FSC-A" = c(min_FSC.A, +Inf))} | ||
| #' @param use_H if \code{TRUE}, gating will be done using \code{height}, | ||
| #' otherwie \code{area} | ||
| #' @param timestamp timestamp. Default: read from \code{sample_metadata.yml} | ||
| #' @param fsa_p1 if \code{NULL}, \code{fsa_p1} will be read in, otherwise the | ||
| #' \code{fsa} | ||
| #' @param fsa_p2 if \code{NULL}, \code{fsa_p2} will be read in, otherwise the | ||
| #' \code{fsa} | ||
| #' @param gates_coordinates if \code{NULL}, \code{gates_coordinates} will be | ||
| #' read in, otherwise the \code{gates_coordinates} | ||
| #' @param wellid_keyword the kwyword which is used to identify the well ID. | ||
| #' Usually "$WELLID" (default), but for the EAWAG Flowcytometer it is "$SMNO". | ||
| #' | ||
| #' @return invisibly \code{TRUE} when completed successful | ||
| #' | ||
| #' @importFrom flowCore read.flowSet pData phenoData exprs logTransform truncateTransform transform | ||
| #' @importFrom flowCore rectangleGate polygonGate Subset | ||
| #' @importFrom yaml read_yaml | ||
| #' @importFrom stats setNames | ||
| #' @importFrom utils read.csv write.csv | ||
| #' @importFrom plyr join | ||
| #' @importFrom tidyr pivot_longer | ||
| #' @importFrom magrittr %>% | ||
| #' @import loggit | ||
| #' @export | ||
| #' | ||
| extract_traits <- function( | ||
| input = NULL, | ||
| particles = c("bacteria", "LNA", "MNA", "HNA", "algae"), | ||
| metadata_flowcytometer, | ||
| min_FSC.A = NULL, | ||
| use_H = FALSE, | ||
| timestamp = yaml::read_yaml(file.path(input, "sample_metadata.yml"))$timestamp, | ||
| fsa_p1 = NULL, | ||
| fsa_p2 = NULL, | ||
| gates_coordinates = NULL, | ||
| wellid_keyword = "$WELLID") { | ||
| message(" reading data ...") | ||
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| if (is.null(fsa_p1)) { | ||
| fsa_p1 <- readRDS(file = file.path(input, paste0("flowcytometer_fsa_ungated.p_1.rds"))) | ||
| } | ||
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| if (is.null(fsa_p2)) { | ||
| fsa_p2 <- readRDS(file = file.path(input, paste0("flowcytometer_fsa_ungated.p_1.rds"))) | ||
| } | ||
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| if (!is.null(min_FSC.A)) { | ||
| g0 <- flowCore::rectangleGate(filterId = "filter_out_0", "FSC-A" = c(min_FSC.A, +Inf)) | ||
| fsa_p1 <- flowCore::Subset(fsa_p1, g0) | ||
| fsa_p2 <- flowCore::Subset(fsa_p2, g0) | ||
| } | ||
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| if (is.null(gates_coordinates)) { | ||
| gates_coordinates <- utils::read.csv(file.path(input, "gates_coordinates.csv")) | ||
| } | ||
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| if (use_H) { | ||
| gates <- calculate_gates_H(gates_coordinates = gates_coordinates) | ||
| } else { | ||
| gates <- calculate_gates(gates_coordinates = gates_coordinates) | ||
| } | ||
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| # function to gate each plate --------------------------------------------- | ||
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| trait_plate <- function(plate_id, | ||
| fsa, | ||
| gates = gates, | ||
| wellid_keyword = wellid_keyword, | ||
| timestamp = timestamp) { | ||
| # extraction function ----------------------------------------------------- | ||
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| extr_traits <- function(pop, | ||
| wellid_keyword = wellid_keyword, | ||
| timestamp = timestamp) { | ||
| traits <- flowCore::fsApply( | ||
| pop, | ||
| function(p) { | ||
| result <- list() | ||
| result$sample <- unlist(flowCore::keyword(p, wellid_keyword)) | ||
| result$plate <- plate_id | ||
| x <- exprs(p) | ||
| if (nrow(x) > 0) { | ||
| result <- suppressWarnings( | ||
| data.frame( | ||
| result, | ||
| x | ||
| ) | ||
| ) | ||
| } else { | ||
| result <- NULL | ||
| } | ||
| return(result) | ||
| } | ||
| ) | ||
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| traits <- do.call(rbind, traits) | ||
| traits$timestamp <- timestamp | ||
| return(traits) | ||
| } | ||
|
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| traits <- list() | ||
| # The Bacteria ------------------------------------------------------------ | ||
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| bacteria_pop <- Subset(fsa, gates$bacteria$bacteria_gate) | ||
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| # LNA_pop <- Subset(bacteria_pop, gates$bacteria$rg_LNA) | ||
| # MNA_pop <- Subset(bacteria_pop, gates$bacteria$rg_MNA) | ||
| # HNA_pop <- Subset(bacteria_pop, gates$bacteria$rg_HNA) | ||
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| traits$bacteria <- extr_traits(bacteria_pop, wellid_keyword = wellid_keyword, timestamp = timestamp) | ||
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| # The Algae --------------------------------------------------------------- | ||
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| algae_pop <- Subset(fsa, gates$algae$algae_gate) | ||
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| traits$algae <- extr_traits(bacteria_pop, wellid_keyword = wellid_keyword, timestamp = timestamp) | ||
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| return(traits) | ||
| } | ||
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| # Do the trait extraction for all plates -------------------------------------------- | ||
|
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| p1 <- trait_plate( | ||
| plate_id = "p_1", | ||
| fsa = fsa_p1, | ||
| gates = gates, | ||
| timestamp = timestamp, | ||
| wellid_keyword = wellid_keyword | ||
| ) | ||
| p2 <- trait_plate( | ||
| plate_id = "p_2", | ||
| fsa = fsa_p2, | ||
| gates = gates, | ||
| timestamp = timestamp, | ||
| wellid_keyword = wellid_keyword | ||
| ) | ||
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| traits <- list() | ||
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| traits$bacteria <- rbind( | ||
| p1$bacteria, | ||
| p2$bacteria | ||
| ) | ||
| traits$algae <- rbind( | ||
| p1$algae, | ||
| p2$algae | ||
| ) | ||
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| traits$bacteria <- merge( | ||
| traits$bacteria, | ||
| metadata_flowcytometer, | ||
| by.x = c("sample", "plate"), | ||
| by.y = c("sample", "plate"), | ||
| all.x = TRUE, | ||
| all.y = FALSE | ||
| ) | ||
| traits$algae <- merge( | ||
| traits$algae, | ||
| metadata_flowcytometer, | ||
| by.x = c("sample", "plate"), | ||
| by.y = c("sample", "plate"), | ||
| all.x = TRUE, | ||
| all.y = FALSE | ||
| ) | ||
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| # Finalize ---------------------------------------------------------------- | ||
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| message(" done") | ||
| message("########################################################") | ||
|
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| return(traits) | ||
| } |
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