plotting all fixed!!

now we can see our fits beautifully

R/browse_evidence.R

@@ -54,10 +54,6 @@ browse_evidence <- function(results.dir = NULL){
           # ppm isn't needed anymore; using spectral matrix ppm.
             lib.data.processed <- lib.data.processed %>% lapply(function(x) {x$data <- NULL; x$ppm <- NULL; return(x)})
 
-            message('*** running patch to map lib.info to lib.data.processed ***')
-            # Library file may not match lib.info (may be smaller, as it is field-specific).
-            # Map them.
-
           # add compound names as column in match.info
             compound.names.refmat <- lapply(lib.data.processed, function(x) x$compound.name) %>% unlist
             match.info$ref.name <- match.info$ref %>% compound.names.refmat[.]
@@ -767,8 +763,10 @@ server <- function(input, output, session) {
                                                                  backfits,
                                                                  rfs.used, # new object with inds of rfs which contributed to scores
                                                                  lib.data.processed,
+                                                                 score.name = 'fsaxrval',
                                                                # # Spectral data:
-                                                               #   xmat, ppm,
+                                                               #   xmat, 
+                                                                 ppm,
                                                                # Filtering thresholds:
                                                                  ppm.tolerance = ppm.tolerance,
                                                                  cutoff.residuals.feat = cutoff.residuals.feat,

R/fastStack.R

@@ -292,7 +292,7 @@ denser_mat_to_df <- function(denser.mat){
 
          # Calculate feature fills
           # Interpolate more x points in
-            browser()
+
             # df.feats <- addpoints_evenly(
             #                              mat = f.stack[, ncol(f.stack):1], # must be increasing xvals
             #                              xvals = rev(ppm[cols.x]),         # must be increasing xvals

R/select_evidence_refmet.R

@@ -37,7 +37,8 @@ select_evidence_refmet <- function(ref = NULL,
                                        lib.data.processed, 
                                        score.name = 'fsaxrval',
                                      # # Spectral data:
-                                     #   xmat, ppm,           
+                                     #   xmat,
+                                       ppm,        
                                      # Filtering thresholds:
                                        ppm.tolerance = pars$matching$filtering$ppm.tol, 
                                        cutoff.residuals.feat = .5,