replace cell with spot in SpatialSeuratApp

Author: Lennart Opitz

master/lib/SpatialSeuratApp.rb

@@ -35,19 +35,19 @@ def initialize
     @params['resolution'] = [0.6, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1]
     @params['resolution', 'description'] = 'Clustering resolution. A higher number will lead to more clusters.'
     @params['nreads'] = ''
-    @params['nreads', 'description'] = 'Low quality cells have less than "nreads" reads. Only when applying fixed thresholds'
+    @params['nreads', 'description'] = 'Low quality spots have less than "nreads" reads. Only when applying fixed thresholds'
     @params['ngenes'] = ''
-    @params['ngenes', 'description'] = 'Low quality cells have less than "ngenes" genes. Only when applying fixed thresholds'
+    @params['ngenes', 'description'] = 'Low quality spots have less than "ngenes" genes. Only when applying fixed thresholds'
     @params['perc_mito'] = ''
-    @params['perc_mito', 'description'] = 'Low quality cells have more than "perc_mito" percent of mitochondrial genes. Only when applying fixed thresholds'
+    @params['perc_mito', 'description'] = 'Low quality spots have more than "perc_mito" percent of mitochondrial genes. Only when applying fixed thresholds'
     @params['perc_ribo'] = ''
-    @params['perc_ribo', 'description'] = 'Low quality cells have more than "perc_ribo" percent of ribosomal genes. Only when applying fixed thresholds'
+    @params['perc_ribo', 'description'] = 'Low quality spots have more than "perc_ribo" percent of ribosomal genes. Only when applying fixed thresholds'
     @params['nmad'] = 3
-    @params['nmad', 'description'] = 'Median absolute deviation (MAD) from the median value of each metric across all cells'
+    @params['nmad', 'description'] = 'Median absolute deviation (MAD) from the median value of each metric across all spots'
     @params['cellsFraction'] = 0.05
-    @params['cellsFraction', 'description'] = 'A gene will be kept if it is expressed in at least this fraction of cells'
+    @params['cellsFraction', 'description'] = 'A gene will be kept if it is expressed in at least this fraction of spots'
     @params['nUMIs'] = 1
-    @params['nUMIs', 'description'] = 'A gene will be kept if it has at least nUMIs in the fraction of cells specified before'
+    @params['nUMIs', 'description'] = 'A gene will be kept if it has at least nUMIs in the fraction of spots specified before'
     @params['specialOptions'] = ''
     @params['mail'] = ""
     @params['Rversion'] = ["Dev/R/4.2.2", "Dev/R/4.2.0", "Dev/R/4.1.2", "Dev/R/4.1.0", "Dev/R/4.0.4", "Dev/R/4.0.3"]