minor changes, ptw, plot

R/align-GCIMSSample.R

@@ -184,8 +184,8 @@ methods::setMethod(
   "alignRt_ptw", "GCIMSSample",
   function(x, ric_ref, ric_ref_rt) {
     optimize_polynomial_order <- function(ric_sample, ric_ref) {
-      correction_type_options <- seq.int(0, 10)
-      poly_orders <- seq.int(1, 10)
+      correction_type_options <- seq.int(0, 2)
+      poly_orders <- seq.int(1, 2)
       xi <- seq_len(length(ric_sample))
       corr <- numeric(length(poly_orders) + 1L)
       corr[1] <- stats::cor(ric_ref, ric_sample, use = "complete.obs")

R/peaks-GCIMSSpectrum.R

@@ -10,7 +10,12 @@ setMethod(
     if (is.null(object@peaks)) {
       stop("Please run findPeaks() on the spectrum first")
     }
-    tibble::as_tibble(cbind(SampleID = object@description, object@peaks))
+    if(nrow(object@peaks)==0){
+      p <- NULL
+    }else{
+      p <- tibble::as_tibble(cbind(SampleID = object@description, object@peaks))
+    }
+    return(p)
   }
 )
 

R/plot-GCIMSSample.R

@@ -74,7 +74,7 @@ mat_to_gplot <- function(intmat, dt_min = NULL, dt_max = NULL, rt_min = NULL, rt
   }
   intmat_trans <- trans$transform(intmat)
   colormap <- farver::encode_native(
-    viridisLite::viridis(256L, direction = -1, option = "A")
+     viridisLite::viridis(256L, direction = -1, option = "G")
   )
   nr <- mat_to_nativeRaster(intmat_trans, colormap)
 
@@ -101,7 +101,7 @@ mat_to_gplot <- function(intmat, dt_min = NULL, dt_max = NULL, rt_min = NULL, rt
     ) +
     ggplot2::scale_fill_viridis_c( # This has to match with the COLORMAP above
       direction = -1,
-      option = "A",
+      option = "G",
       limits = minmax,
       na.value = "#00000000",
       trans = trans