Add smooth fit span and number of points parameters

rajewsky-lab · May 17, 2018 · 146caf5 · 146caf5
1 parent ac8dc1a
commit 146caf5
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Showing 2 changed files with 23 additions and 3 deletions.
diff --git a/functions.R b/functions.R
@@ -21,7 +21,7 @@
 # file:         functions.R
 # author(s):    Marcel Schilling <marcel.schilling@mdc-berlin.de>
 # created:      2017-02-23
-# last update:  2018-01-05
+# last update:  2018-02-27
 # license:      GNU Affero General Public License Version 3 (GNU AGPL v3)
 # purpose:      define functions for tomo-seq shiny app
 
@@ -30,6 +30,7 @@
 # change log (reverse chronological) #
 ######################################
 
+# 2018-02-27: added usage of smooth fit span and number of points parameters
 # 2018-01-05: switched from identifying transcripts by name to isoform number (for color assignment)
 #             (identied as part after the last dot (".") in the transcript name; this enables
 #             re-using the same color for different genes)
@@ -945,6 +946,12 @@ plot.profiles<-
               # adjust smoothing method
               ,method=params$profile.plot.smoothing.method
 
+              # adjust smoothing span
+              ,span=params$profile.plot.smoothing.span
+
+              # adjust number of smoothing points
+              ,n=params$profile.plot.smoothing.n
+
               # adjust smooth line size
               ,size=params$profile.plot.linesize.each
 
@@ -966,6 +973,12 @@ plot.profiles<-
               # adjust smoothing method
               ,method=params$profile.plot.smoothing.method
 
+              # adjust smoothing span
+              ,span=params$profile.plot.smoothing.span
+
+              # adjust number of smoothing points
+              ,n=params$profile.plot.smoothing.n
+
               # adjust smooth line size
               ,size=params$profile.plot.linesize.pooled
 

diff --git a/params.R b/params.R
@@ -1,5 +1,5 @@
 # tomo-seq shiny app parameter definition script
-# Copyright (C) 2017  Marcel Schilling
+# Copyright (C) 2017-2018  Marcel Schilling
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU Affero General Public License as
@@ -21,7 +21,7 @@
 # file:         params.R
 # author(s):    Marcel Schilling <marcel.schilling@mdc-berlin.de>
 # created:      2017-02-21
-# last update:  2017-10-23
+# last update:  2018-02-27
 # license:      GNU Affero General Public License Version 3 (GNU AGPL v3)
 # purpose:      define parameters for tomo-seq shiny app
 
@@ -30,6 +30,7 @@
 # change log (reverse chronological) #
 ######################################
 
+# 2018-02-27: added smooth fit span and number of points parameters
 # 2017-10-23: replaced smooth fit color parameter by linetype parameter (color now used for
 #             isoforms)
 #             added isoform level input panel parameters / added isoform legend parameter for
@@ -505,6 +506,12 @@ if(!exists("params"))
       # data smoothing method of profile plot
       ,profile.plot.smoothing.method="loess"
 
+      # data smoothing span of profile plot
+      ,profile.plot.smoothing.span=.75
+
+      # number of data smoothing points of profile plot
+      ,profile.plot.smoothing.n=80
+
 
       ##############
       # appearance #