Merge pull request #5 from andcastillo/patch-1

Create visualize.NMRium.R
jwist · Dec 29, 2023 · 817df52 · 817df52
2 parents 21c1620 + cd26ebb
commit 817df52
Showing 1 changed file with 97 additions and 0 deletions.
diff --git a/R/visualize.NMRium.R b/R/visualize.NMRium.R
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+#' Method for exporting spectra information into the NMRium format. You can use this to export simple x, re and x, re and im spectra
+#' If you provide a list containing NMRium data, it will append the new spectra data into the proper place, 
+#' so that you can get an overlay of several spectra into the platform. 
+#'
+#' @param x Independent variable
+#' @param yr Real dependent variable
+#' @param yi (optional)Imaginary dependent variable
+#' @param output Object containing other NMRium data
+#' @param observeFrequency Observe frequency in MHz
+#' @param dataTypeData Data type format. Use 'NMR FID' if the spectrum is in the time domain (Default 'NMR SPECTRUM')
+#' @param solvent String that specify the solvent. (Default 'UNKNOWN') 
+#' @param nucleus Observe nucleus.  (Default '1H') 
+#' @param PHC0 Phase 0 correction value (Optional, Default 0)
+#' @param PHC1 Phase 1 correction value (Optional, Default 0)
+#' @param col Color for this spectrum(Default black)
+
+#' @return list
+#' @examples
+#'
+#' nmrium <- exportReIm(ppm, Y[1,], NULL, output=NA, observeFrequency=600, dataType='NMR SPECTRUM', solvent='UNKNOWN', nucleus='1H', PHC0=0, PHC1=0, col='#AA0109')
+#' nmrium <- exportReIm(ppm, Y[2,], NULL, output=nmrium, observeFrequency=600, dataType='NMR SPECTRUM', solvent='UNKNOWN', nucleus='1H', PHC0=0, PHC1=0, col='#0000FF')
+#' nmrium <- exportReIm(ppm, Y[3,], NULL, output=nmrium, observeFrequency=600, dataType='NMR SPECTRUM', solvent='UNKNOWN', nucleus='1H', PHC0=0, PHC1=0, col='#FFFF00')
+#' nmrium <- exportReIm(ppm, Y[4,], NULL, output=nmrium, observeFrequency=600, dataType='NMR SPECTRUM', solvent='UNKNOWN', nucleus='1H', PHC0=0, PHC1=0, col='#00AA00')
+#' 
+#' write(toJSON(nmrium, pretty = TRUE, auto_unbox = TRUE, digits = 12), file='export.nmrium')
+#'
+#' @export
+exportReIm <- function(x, yr, yi, output=NA, observeFrequency=600, dataType='NMR SPECTRUM', solvent='UNKNOWN', nucleus='1H', PHC0=0, PHC1=0, col='#000000') {
+  meta <- list("TITLE"="spectra-data from ReIm",
+               "JCAMPDX"="5.00 $$Cheminfo tools 3.4.11",
+               "OWNER"="",
+               "DATATYPE"="NMR SPECTRUM",
+               "DATACLASS"="XYDATA",
+               "OBSERVEFREQUENCY"=observeFrequency,
+               ".OBSERVENUCLEUS"= nucleus,
+               ".SOLVENTNAME"=solvent,
+               "XUNITS"="PPM",
+               "YUNITS"="Intensity",
+               "NPOINTS"=length(x),
+               "FIRSTX"=x[[1]],
+               "LASTX"=x[[length(x)]],
+               "FIRSTY"=yr[[1]],
+               "LASTY"=yr[[length(yr)]],
+               "XFACTOR"=(x[[length(x)]] - x[[1]]) / (length(x) - 1),
+               "YFACTOR"=1,
+               "MAXY"=max(yr),
+               "MINY"=min(yr),
+               "DELTAX"=(x[[length(x)]] - x[[1]]) / (length(x) - 1),
+               "DECIM"=0,
+               "DSPFVS"=0,
+               "FCOR"=0,
+               "SW_h"=(x[[length(x)]] - x[[1]]) * observeFrequency,
+               "SW"=(x[[length(x)]] - x[[1]]),
+               "TD"=length(x),
+               "DSPFVS"=0,
+               "BF1"=0,
+               "SFO1"=observeFrequency,
+               "NUC1"=paste0("<",nucleus,">"),
+               "PHC0"=PHC0,
+               "PHC1"=PHC1)
+  info <- list("nucleus"= nucleus,
+               "isFid"=FALSE,
+               "isComplex"=TRUE,
+               "dimension"=1,
+               "name"="",
+               "isFt"=TRUE,
+               "experiment"="",
+               "fnMode"="undefined",
+               "title"="spectra-data from ReIm",
+               "solvent"=solvent,
+               "type"="NMR SPECTRUM",
+               "dataClass"="XYDATA",
+               "firstX"=x[[1]],
+               "lastX"=x[[length(x)]],
+               "numberOfPoints"=length(x),
+               "originFrequency"=observeFrequency,
+               "baseFrequency"=0,
+               "fieldStrength"=0,
+               "spectralWidth"=(x[[length(x)]] - x[[1]]),
+               "acquisitionTime"=length(x)/(2*observeFrequency*(x[[length(x)]] - x[[1]])),
+               "groupDelay"=0,
+               "DECIM"=0,
+               "DSPFVS"=0,
+               "increment"=(x[[length(x)]] - x[[1]]) / (length(x) - 1),
+               "frequencyOffset"=observeFrequency*1e6,              
+               "PHC0"=PHC0,
+               "PHC1"=PHC1)
+  data <- list("x"=x, "re"=yr, "im"=yi)
+  display <- list("color"=col, "isPeaksMarkersVisible"=TRUE, "isRealSpectrumVisible"=TRUE,"isVisible"=TRUE, "isVisibleInDomain"=TRUE)
+
+  if(all(is.na(output))) {
+    return (list("version"=4, "data"=list("spectra"=list(list("data"=data, "meta"=meta, "info"=info, "display"=display)))))
+  } else {
+    output[["data"]][["spectra"]] <- append(output[["data"]][["spectra"]], list(list("data"=data, "meta"=meta, "info"=info, "display"=display)))
+    return(output)
+  }
+}