Added arguments to limit user interaction
This commit is contained in:
Waldir Leoncio
parent
b622375062
commit
3fcd4affcb
2 changed files with 83 additions and 35 deletions
107
R/greedyMix.R
107
R/greedyMix.R
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@ -1,7 +1,14 @@
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#' @title Clustering of individuals
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#' @param tietue Record
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#' @param format Format of the data ("BAPS", "GenePop" or "Preprocessed")
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#' @param savePreProcessed Save the pre-processed data?
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#' @export
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greedyMix <- function(tietue) {
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greedyMix <- function(
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tietue,
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format = NULL,
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savePreProcessed = NULL,
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filePreProcessed = NULL
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) {
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# ASK: graphical components. Remove?
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# check whether fixed k mode is selected
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# h0 <- findobj('Tag','fixk_menu')
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@ -17,32 +24,46 @@ greedyMix <- function(tietue) {
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# h1 = findobj('Tag','partitioncompare_menu');
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# partitionCompare = get(h1, 'userdata');
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if (identical(tietue, -1)) {
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input_type <- inputdlg(
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paste(
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'Specify the format of your data:\n',
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'1) BAPS-format\n',
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'2) GenePop-format\n',
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'3) Preprocessed data\n'
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if (is(tietue, "list") | is(tietue, "character")) {
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# ----------------------------------------------------------------------
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# Defining type of file
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# ----------------------------------------------------------------------
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if (is.null(format)) {
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input_type <- inputdlg(
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paste(
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'Specify the format of your data:\n',
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'1) BAPS-format\n',
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'2) GenePop-format\n',
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'3) Preprocessed data\n'
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)
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)
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)
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# Converting from number into name
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input_type_name <- switch(
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input_type, 'BAPS-format', 'GenePop-format', 'Preprocessed data'
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)
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# Converting from number into name
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input_type_name <- switch(
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input_type, 'BAPS-format', 'GenePop-format', 'Preprocessed data'
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)
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} else {
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input_type_name <- paste0(format, "-format")
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}
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# ----------------------------------------------------------------------
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# Treating BAPS-formatted files
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# ----------------------------------------------------------------------
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if (length(input_type_name) == 0) {
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stop('Invalid alternative')
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} else if (input_type_name == 'BAPS-format') {
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pathname_filename <- uigetfile("*.txt", "Loaddata in BAPS-format")
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if (!is(tietue, "character")) {
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pathname_filename <- uigetfile("*.txt", "Loaddata in BAPS-format")
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} else {
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pathname_filename <- tietue
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}
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# ASK: remove?
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# if ~isempty(partitionCompare)
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# fprintf(1,'Data: %s\n',[pathname filename]);
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# end
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data <- load(pathname_filename)
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data <- read.delim(pathname_filename) # ASK: what is the delimiter?
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# ninds <- testaaOnkoKunnollinenBapsData(data) #TESTAUS # TODO: trans
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if (ninds == 0) stop('Incorrect Data-file')
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# if (ninds == 0) stop('Incorrect Data-file')
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# ASK: remove?
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# h0 = findobj('Tag','filename1_text');
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@ -78,13 +99,16 @@ greedyMix <- function(tietue) {
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# [data, rowsFromInd, alleleCodes, noalle, adjprior, priorTerm] = handleData(data); # TODO: translate this function
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# [Z,dist] = newGetDistances(data,rowsFromInd); # TODO: translate
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save_preproc <- questdlg(
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quest = 'Do you wish to save pre-processed data?',
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dlgtitle = 'Save pre-processed data?',
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defbtn = 'y'
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)
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if (save_preproc %in% c('y', 'yes')) {
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if (is.null(savePreProcessed)) {
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save_preproc <- questdlg(
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quest = 'Do you wish to save pre-processed data?',
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dlgtitle = 'Save pre-processed data?',
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defbtn = 'y'
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)
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} else {
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save_preproc <- savePreProcessed
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}
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if (save_preproc %in% c('y', 'yes', TRUE)) {
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file_out <- uiputfile('.rda','Save pre-processed data as')
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kokonimi <- paste0(file_out$path, file_out$name)
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c <- list()
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@ -100,12 +124,19 @@ greedyMix <- function(tietue) {
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save(c, file = kokonimi)
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rm(c)
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}
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# ----------------------------------------------------------------------
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# Treating GenePop-formatted files
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# ----------------------------------------------------------------------
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} else if (input_type_name == 'GenePop-format') {
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filename_pathname <- uigetfile(
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filter = '*.txt',
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title = 'Load data in GenePop-format'
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)
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if (filename_pathname$name == 0) stop("No name provided")
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if (!is(tietue, "character")) {
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filename_pathname <- uigetfile(
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filter = '*.txt',
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title = 'Load data in GenePop-format'
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)
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if (filename_pathname$name == 0) stop("No name provided")
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} else {
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filename_pathname <- tietue
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}
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# ASK: remove?
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# if ~isempty(partitionCompare)
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@ -121,14 +152,19 @@ greedyMix <- function(tietue) {
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# [data, rowsFromInd, alleleCodes, noalle, adjprior, priorTerm] = handleData(data); # TODO:trans
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# [Z,dist] = newGetDistances(data,rowsFromInd); # TODO: trans
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save_preproc <- questdlg(
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quest = 'Do you wish to save pre-processed data?',
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dlgtitle = 'Save pre-processed data?',
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defbtn = 'y'
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)
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if (save_preproc %in% c('y', 'Yes')) {
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if (is.null(savePreProcessed)) {
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save_preproc <- questdlg(
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quest = 'Do you wish to save pre-processed data?',
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dlgtitle = 'Save pre-processed data?',
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defbtn = 'y'
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)
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} else {
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save_preproc <- savePreProcessed
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}
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if (save_preproc %in% c('y', 'Yes', TRUE)) {
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file_out <- uiputfile('.rda','Save pre-processed data as')
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kokonimi <- paste0(file_out$path, file_out$name)
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# FIXME: translate functions above so the objects below exist
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c$data <- data
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c$rowsFromInd <- rowsFromInd
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c$alleleCodes <- alleleCodes
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@ -141,6 +177,9 @@ greedyMix <- function(tietue) {
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save(c, file = kokonimi)
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rm(c)
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}
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# ----------------------------------------------------------------------
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# Handling Pre-processed data
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# ----------------------------------------------------------------------
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} else if (input_type_name == 'Preprocessed data') {
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file_in <- uigetfile(
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filter = '*.txt',
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@ -4,10 +4,19 @@
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\alias{greedyMix}
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\title{Clustering of individuals}
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\usage{
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greedyMix(tietue)
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greedyMix(
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tietue,
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format = NULL,
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savePreProcessed = NULL,
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filePreProcessed = NULL
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)
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}
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\arguments{
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\item{tietue}{Record}
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\item{format}{Format of the data ("BAPS", "GenePop" or "Preprocessed")}
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\item{savePreProcessed}{Save the pre-processed data?}
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}
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\description{
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Clustering of individuals
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