Fixed issue num 1, heatmap ranges.

R/GCAT/R/plot.fit.R

@@ -304,6 +304,9 @@ plot_residuals = function(input.well, xlim = NULL, lowess = T, ...){
 #' @return path of heatmap pdf file
 #' 
 create.heatmap = function(fitted.well.array, attribute, MinMax = NA, unlog=NULL){
+  # debug
+  #browser()
+  
   attr.name <- deparse(substitute(attribute))
   pdf.name <- ""
   if(class(fitted.well.array) == "matrix"){
@@ -319,9 +322,9 @@ create.heatmap = function(fitted.well.array, attribute, MinMax = NA, unlog=NULL)
     num.dig = 3 #how many digits should be put on pdf?
     max = round(max(spec.growth, na.rm=T), digits=num.dig)
     min = round(min(spec.growth, na.rm=T), digits=num.dig)
-    avg = round(mean(spec.growth, na.rm=T), digits=num.dig)
+    avg = round(median(spec.growth, na.rm=T), digits=num.dig)
     heat.text = paste(toupper(sub("\\.", " ", attr.name)), ":\n", plate.ID, "\n",
-                                            paste("Max:",max ,"Min:" ,min ,"Avg:", avg, sep=""))
+                      paste("Min:", min, "Med:", avg, "Max:", max, sep=" "))
                       
     attr.name <- sub("\\.", "_", attr.name) #do not want periods in file path
     letters <- attr(fitted.well.array, "dimnames")[[1]]
@@ -334,16 +337,13 @@ create.heatmap = function(fitted.well.array, attribute, MinMax = NA, unlog=NULL)
     #heatmap(heat, Rowv=NA, Colv=NA, revC=T, scale="none", na.rm=T, main=plate.ID, col=rainbow(100), margins=c(6,6))
     #mtext(paste("Max:", round(max(spec.growth, na.rm=T), digits=4),"Min:", round(min(spec.growth, na.rm=T), digits=4), "Avg:", round(mean(spec.growth, na.rm=T), digits=4)), side=1, line=3)
     if (length(MinMax) == 2){
-      Mean = mean(MinMax)
+      #  Min and max values to plot to floor and ceiling values if MinMax parameter was specified by the caller
-      bk = unique(c(seq(MinMax[1], Mean, length=50), seq(Mean, MinMax[2], length = 50)))
+      heat[is.finite(heat) & heat < MinMax[1]] = MinMax[1]
-      pheatmap(heat, color=colorpanel(100, "red", "orange", "yellow"), breaks = bk,
+      heat[is.finite(heat) & heat > MinMax[2]] = MinMax[2]
-               border_color="black", cell_width=2, cell_height=3,
+    }
-               cluster_rows=F, cluster_cols=F, scale='none', main=heat.text, fontsize=16)
-    } else {
     pheatmap(heat, color=colorpanel(100, "red", "orange", "yellow"),
              border_color="black", cell_width=2, cell_height=3,
              cluster_rows=F, cluster_cols=F, scale='none', main=heat.text, fontsize=16)
-    }
     dev.off()
   }
   else {

R/GCAT/inst/extdata/heatmap_tests/test_heatmap_limits.R

@@ -0,0 +1,20 @@
+#  Test that heatmaps are processed and generated correctly
+#  Yury V Bukhman, 01 July 2015
+#  This script generates heat maps with pre-set limits.  Manually check output directory to see if they make sense.
+
+INPUT.DIR =  system.file("extdata/YPDAFEXglucoseTests_2-25-10",package="GCAT")
+OUTPUT.DIR = paste(system.file("extdata/heatmap_tests",package="GCAT"),"temp",sep="/")
+INPUT.FILE = "YPDAFEXglucoseTests_2-25-10.csv"
+
+#  Run GCAT
+library(GCAT)
+setwd(INPUT.DIR)
+time.input=1/3600
+out = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL,   
+                         out.dir = OUTPUT.DIR, graphic.dir = OUTPUT.DIR, 
+                         add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,
+                         use.linear.param=F, use.loess=F, smooth.param=0.1,
+                         points.to.remove = integer(), remove.jumps = F, time.input=time.input,
+                         silent = F, verbose = T, return.fit = T, overview.jpgs = T,
+                         lagRange = c(0,3), totalRange = c(0.2,0.82), specRange = c(0.04,0.13))
+