From 91bd92db52a9a5496283559adf4b7b2c3f3a524f Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Fri, 27 May 2022 11:11:05 +0200
Subject: [PATCH] update R wrapper

---
 R/PCAone.R | 104 +++++++++++++++++++++++++++++++++--------------------
 1 file changed, 66 insertions(+), 38 deletions(-)

diff --git a/R/PCAone.R b/R/PCAone.R
index 4d32200..16dc81c 100644
--- a/R/PCAone.R
+++ b/R/PCAone.R
@@ -1,61 +1,89 @@
 ## R wrapper for PCAone
 library(data.table)
-PCAone <- function (
-                    program = "PCAone",
-                    k = 10,
-                    bfile = NULL,
-                    bgen  = NULL,
-                    beagle = NULL,
-                    out = tempfile(),
-                    arnoldi = FALSE,
-                    threads = 1,
-                    fast = FALSE,
-                    emu = FALSE,
-                    pcangsd = FALSE,
-                    memory = 0,
-                    maxp = 20,
-                    bands = 128,
-                    verbose = FALSE,
-                    tol_em = 1e-5,
-                    tol_maf =  1e-4,
-                    tol_halko = 1e-4,
-                    maxiter = 100,
-                    imaxiter = 1000,
-                    itol = 1e-6,
-                    ncv = 20
-                    ) {
+PCAone <- function(program = "PCAone",
+                   k = 10,
+                   bfile = NULL,
+                   bgen = NULL,
+                   beagle = NULL,
+                   csv = NULL,
+                   arnoldi = TRUE,
+                   fast = FALSE,
+                   halko = FALSE,
+                   out = tempfile(),
+                   cpmed = FALSE,
+                   printv = FALSE,
+                   shuffle = FALSE,
+                   emu = FALSE,
+                   pcangsd = FALSE,
+                   threads = 1,
+                   memory = 0,
+                   maxp = 20,
+                   oversamples = 10,
+                   bands = 64,
+                   tol_em = 1e-4,
+                   tol_maf = 1e-4,
+                   tol_rsvd = 1e-4,
+                   maxiter = 100,
+                   imaxiter = 1000,
+                   itol = 1e-6,
+                   ncv = 20,
+                   tmp = NULL,
+                   verbose = FALSE) {
+  if (file.exists(paste0(out, ".eigvecs")) && file.exists(paste0(out, ".eigvals"))) {
+    if (printv) {
+      res <- list(u = as.matrix(fread(paste0(out, ".eigvecs"))), d = as.vector(fread(paste0(out, ".eigvals"))[,1]), v = as.matrix(fread(paste0(out, ".loadings"))))
+    } else {
+      res <- list(u = as.matrix(fread(paste0(out, ".eigvecs"))), d = as.vector(fread(paste0(out, ".eigvals"))[,1]))
+    }
+
+    return(res)
+  }
   infile <- NULL
   if (!is.null(bfile)) infile <- paste("--bfile", bfile)
   if (!is.null(bgen)) infile <- paste("--bgen", bgen)
   if (!is.null(beagle)) infile <- paste("--beagle", beagle)
+  if (!is.null(csv)) infile <- paste("--csv", csv)
   stopifnot(!is.null(infile))
 
-  callCmds <- paste(infile, "-k", k, "-n", threads, "-o", out)
-  if (memory > 0) callCmds <- paste(callCmds, "-m", memory)
+  callCmds <- paste(
+    infile, "-k", k, "-n", threads, "-o", out
+  )
   if (arnoldi) {
     callCmds <- paste(callCmds, "-a")
-  } else {
-    callCmds <- paste(callCmds, "--maxp", maxp)
-    if (fast) callCmds <- paste(callCmds, "-f")
+  } else if (fast) {
+    callCmds <- paste(callCmds, "-f")
+  } else if (halko) {
+    callCmds <- paste(callCmds, "-h")
   }
   if (emu) {
     callCmds <- paste(callCmds, "--emu")
   } else if (pcangsd) {
     callCmds <- paste(callCmds, "--pcangsd")
   }
-  if (verbose) callCmds <- paste(callCmds, "-v")
-  if (tol_em != 1e-5) callCmds <- paste(callCmds, "--tol-em", tol_em)
+  if (!is.null(tmp)) callCmds <- paste(callCmds, "--tmp", tmp)
+  if (memory > 0) callCmds <- paste(callCmds, "-m", memory)
+  if (ncv != 20) callCmds <- paste(callCmds, "--ncv", ncv)
+  if (maxp != 20) callCmds <- paste(callCmds, "--maxp", maxp)
+  if (bands != 64) callCmds <- paste(callCmds, "--bands", bands)
+  if (tol_rsvd != 1e-4) callCmds <- paste(callCmds, "--tol-rsvd", tol_rsvd)
+  if (tol_em != 1e-4) callCmds <- paste(callCmds, "--tol-em", tol_em)
   if (tol_maf != 1e-4) callCmds <- paste(callCmds, "--tol-maf", tol_maf)
-  if (tol_halko != 1e-4) callCmds <- paste(callCmds, "--tol-halko", tol_halko)
   if (itol != 1e-6) callCmds <- paste(callCmds, "--itol", itol)
   if (maxiter != 100) callCmds <- paste(callCmds, "--maxiter", maxiter)
-  if (imaxiter != 1000) callCmds <- paste(callCmds, "--imaxiter", imaxiter)
-  if (ncv != 20) callCmds <- paste(callCmds, "--ncv", ncv)
+  if (imaxiter != 100) callCmds <- paste(callCmds, "--imaxiter", imaxiter)
+  if (oversamples != 10) callCmds <- paste(callCmds, "--oversamples", oversamples)
+  if (printv) callCmds <- paste(callCmds, "--printv")
+  if (shuffle) callCmds <- paste(callCmds, "--shuffle")
+  if (verbose) callCmds <- paste(callCmds, "-v")
 
   print(paste("Calling:", program, callCmds))
   ## system2(program, callCmds, stdout = paste0(out, ".o"), stderr = paste0(out, ".e"))
-  system2(program, callCmds, stdout = paste0(out, ".log"))
-  U <- fread(paste0(out, ".eigvecs"))
-  S <- fread(paste0(out, ".eigvals"))
-  res <-  list(u = as.matrix(U), d = as.vector(S$V1))
+  system2(program, callCmds, stdout = paste0(out, ".llog"))
+  if (printv) {
+    res <- list(u = as.matrix(fread(paste0(out, ".eigvecs"))), d = as.vector(fread(paste0(out, ".eigvals"))[,1]), v = as.matrix(fread(paste0(out, ".loadings"))))
+  } else {
+    res <- list(u = as.matrix(fread(paste0(out, ".eigvecs"))), d = as.vector(fread(paste0(out, ".eigvals"))[,1]))
+  }
+
+  return(res)
 }