fix(dataProcessPlots): Change default of ylimDown to minimum of log2 intensity - 3

Author: tonywu1999

R/dataProcessPlotsPTM.R

@@ -29,7 +29,8 @@
 #' FALSE(Default) for Profile Plot and QC Plot uses the upper limit as rounded
 #' off maximum of log2(intensities) after normalization + 3..
 #' @param ylimDown lower limit for y-axis in the log scale. FALSE(Default) for
-#' Profile Plot and QC Plot uses 0..
+#' Profile Plot and QC Plot uses the lower limit as floor of minimum
+#' log2(intensities) after normalization - 3, or 0 if that value is negative.
 #' @param x.axis.size size of x-axis labeling for "Run" and "channel in Profile
 #' Plot and QC Plot.
 #' @param y.axis.size size of y-axis labels. Default is 10.

R/utils_dataProcessPlots.R

@@ -553,11 +553,12 @@
   if (is.numeric(ylimDown)) {
     y.limdown = ylimDown
   } else {
-    y.limdown = 0
+    all_abund = if (plot_global) c(datafeature.ptm$ABUNDANCE, datafeature.protein$ABUNDANCE) else datafeature.ptm$ABUNDANCE
+    y.limdown = max(floor(min(all_abund, na.rm = TRUE) - 3), 0)
   }
-  
+
   ## Apply pre-plot formatting
-  ptm.list = .preplot.format.tmt(datafeature.ptm, datarun.ptm, 
+  ptm.list = .preplot.format.tmt(datafeature.ptm, datarun.ptm,
                                        y.limup, type)
   datafeature.ptm = ptm.list[[1]]
   datarun.ptm = ptm.list[[2]]
@@ -871,13 +872,15 @@
     y.limup = ylimUp
   }
 
-  y.limdown = 0
   if (is.numeric(ylimDown)) {
     y.limdown = ylimDown
+  } else {
+    all_abund = if (length(data.table.list) == 4) c(datafeature.ptm$ABUNDANCE, datafeature.protein$ABUNDANCE) else datafeature.ptm$ABUNDANCE
+    y.limdown = max(floor(min(all_abund, na.rm = TRUE) - 3), 0)
   }
-  
+
   ## Apply pre-plot formatting
-  ptm.list = .preplot.format.tmt(datafeature.ptm, datarun.ptm, y.limup, 
+  ptm.list = .preplot.format.tmt(datafeature.ptm, datarun.ptm, y.limup,
                                        type)
   datafeature.ptm = ptm.list[[1]]
   datarun.ptm = ptm.list[[2]]
@@ -1374,10 +1377,11 @@
   if (is.numeric(ylimDown)) {
     y.limdown = ylimDown
   } else {
-    y.limdown = 0
+    all_abund = if (plot_global) c(datafeature.ptm$ABUNDANCE, datafeature.protein$ABUNDANCE) else datafeature.ptm$ABUNDANCE
+    y.limdown = max(floor(min(all_abund, na.rm = TRUE) - 3), 0)
   }
-  
-  ptm.list = .preplot.format.lf(datafeature.ptm, datarun.ptm, 
+
+  ptm.list = .preplot.format.lf(datafeature.ptm, datarun.ptm,
                                   y.limup, type)
   datafeature.ptm = ptm.list[[1]]
   datarun.ptm = ptm.list[[2]]
@@ -1667,11 +1671,13 @@
     y.limup = ylimUp
   }
 
-  y.limdown = 0
   if (is.numeric(ylimDown)) {
     y.limdown = ylimDown
+  } else {
+    all_abund = if (length(data.table.list) == 4) c(datafeature.ptm$ABUNDANCE, datafeature.protein$ABUNDANCE) else datafeature.ptm$ABUNDANCE
+    y.limdown = max(floor(min(all_abund, na.rm = TRUE) - 3), 0)
   }
-  
+
   ## Apply pre-plot formatting
   ptm.list = .preplot.format.lf(datafeature.ptm, datarun.ptm, y.limup, type)
   datafeature.ptm = ptm.list[[1]]