rbbt-util 5.21.77 → 5.21.78

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 94b444c704c00b00fa41fc21ecda0eac99065d37
-  data.tar.gz: d4c01b71ab11e74c7fb0c25822246688323c7e26
+  metadata.gz: 79f060e03080aa195d6e1c4372dd004653ed8801
+  data.tar.gz: 0af2cbb746b785018adbc4b37e377a74f84def35
 SHA512:
-  metadata.gz: 9b41bd6356dcd57efdf98f0540af944b2e058b96a232ce5c724a2cba9767b5612464c5c3d9b5c5760b0b34f1bd2f7dd2ba800a642141ce8df7c13ae17984a2b7
-  data.tar.gz: fc5b7a8b16b9b11ebf2d7906500016bc4416f0689fd64fadc31dd07e28f8bc1513a64c6dbfe80cca52d669bddb66ad01b5d51ba3d3b97174c35348286d79c502
+  metadata.gz: 5c791b7f553c8bc32512c7eab3bffc9d94bf072d878f5daf32dd0afc7a2e87b7cfcc290bab5430c99c715e7672856d1007bae8b6501aa71eb7f211b820a36b66
+  data.tar.gz: 4af9194d609ee3537a4add26274448316976a61f8f9064f7f0cadb9f37b8db0784cf3f3b4469ceb9a15324934e92e67e795b4ee07e0834801ba94c82fcb09500

data/lib/rbbt/persist.rb

@@ -286,6 +286,9 @@ module Persist
         else
           Open.rm path if Open.exists? path
         end
+      rescue Aborted, Interrupt
+        Log.warn "Aborted loading persistence (#{ type }) #{ path }: #{$!.message}. Not erasing."
+        raise $!
       rescue Exception
         Log.warn "Exception loading persistence (#{ type }) #{ path }: #{$!.message}. Erase and retry."
         Open.rm path if Open.exists? path

data/lib/rbbt/tsv/accessor.rb

@@ -694,7 +694,7 @@ Example:
             if new.include? k
               new[k] = Misc.zip_fields(Misc.zip_fields(new[k]) << rest)
             else
-              new[k] = rest.collect{|v| [v]}
+              new[k] = rest.nil? ? nil : rest.collect{|v| [v]}
             end
           end
         end

data/lib/rbbt/tsv/manipulate.rb

@@ -166,13 +166,18 @@ module TSV
     traverser = Traverser.new key_field, fields, new_key_field, new_fields, type, uniq
 
     if @monitor
-      desc = "Iterating TSV"
-      step = 100
-      if Hash === @monitor
-        desc = @monitor[:desc] if @monitor.include? :desc 
-        step = @monitor[:step] if @monitor.include? :step 
+      if Log::ProgressBar === @monitor
+        @monitor.max = size
+        progress_monitor = @monitor
+      else
+        desc = "Iterating TSV"
+        step = 100
+        if Hash === @monitor
+          desc = @monitor[:desc] if @monitor.include? :desc 
+          step = @monitor[:step] if @monitor.include? :step 
+        end
+        progress_monitor = Log::ProgressBar.new_bar(size, :desc => desc)
       end
-      progress_monitor = Log::ProgressBar.new_bar(size, :desc => desc)
     else
       progress_monitor = nil
     end

data/lib/rbbt/util/R.rb

@@ -198,13 +198,14 @@ NULL
     end
   end
 
-  def R_interactive(pre_script = nil)
+  def R_interactive(pre_script = nil, source = true)
     TmpFile.with_file do |f|
       Log.debug{"R Interactive:\n" << pre_script } if pre_script
       TmpFile.with_file(pre_script) do |script_file|
         Open.write(f, self.to_s)
         script = "data_file = '#{f}';\n"
         script << "script_file = '#{script_file}';\n" if pre_script
+        script << "source(script_file);\n" if source
         R.interactive(script)
       end
     end

data/lib/rbbt/util/colorize.rb

@@ -13,12 +13,16 @@ module Colorize
       colors["green3"] 
     when 'red'
       colors["red3"] 
+    when 'yellow'
+      colors["gold1"] 
+    when 'blue'
+      colors["RoyalBlue"] 
     else
       colors[color.to_s] || color
     end
   end
 
-  def self.continuous(array, start = :green, eend = :red, percent = false) 
+  def self.continuous(array, start = "#EABD5D", eend = "#40324F", percent = false) 
     start_color = Color.new from_name(start)
     end_color = Color.new from_name(eend)
 
@@ -70,7 +74,7 @@ module Colorize
 
   def self.tsv(tsv, options = {})
     values = tsv.values.flatten
-    if Fixnum === values.first or (values.first.to_f != 0 and values[0] != "0")
+    if Fixnum === values.first or Float === values.first or (values.first.to_f != 0 and values[0] != "0" and values[0] != "0.0")
       value_colors = Misc.process_to_hash(values){continuous(values)}
     else
       value_colors = Misc.process_to_hash(values){distinct(values)}

data/lib/rbbt/workflow/accessor.rb

@@ -100,7 +100,7 @@ class Step
   end
 
   def info(check_lock = true)
-    return {} if info_file.nil? or not Open.exists? info_file
+    return {:status => :noinfo} if info_file.nil? or not Open.exists? info_file
     begin
       Misc.insist do
         begin
@@ -351,8 +351,10 @@ class Step
   end
 
   def dirty?
-    return true if done? and not status == :done
-    dirty_files = rec_dependencies.collect{|dependency| dependency.path unless dependency.error? and not dependency.recoverable_error? }.compact.uniq.reject{|path| not (Path === path) or path.exists?}
+    status = self.status
+    return true if done? and not status == :done and not status == :noinfo
+    return true if status == :done and not done?
+    dirty_files = rec_dependencies.collect{|dependency| dependency.path unless dependency.error? and not dependency.recoverable_error? }.compact.uniq.reject{|path| ! (Path === path) || path.exists?}
     if dirty_files.any?
       true
     else

data/lib/rbbt/workflow/step.rb

@@ -61,6 +61,24 @@ class Step
     @inputs
   end
 
+  def recursive_inputs
+    if NamedArray === inputs
+      i = Hash[*inputs.fields.zip(inputs).flatten]
+    else
+      i = {}
+    end
+    dependencies.each do |dep|
+      di = dep.recursive_inputs
+      next unless NamedArray === di
+      di.fields.zip(di).each do |k,v|
+        i[k] = v unless i.include? k
+      end
+    end
+    v = i.values
+    NamedArray.setup v, i.keys 
+    v
+  end
+
   def task_name
     @task.name
   end

data/lib/rbbt/workflow/step/dependencies.rb

@@ -83,7 +83,7 @@ class Step
       return if status == 'streaming' and job.running?
     end
 
-    if (status == 'error' || job.aborted?) && job.recoverable_error?
+    if ((status == 'error' || job.aborted?) && job.recoverable_error?) || job.dirty?
       job.clean 
     end
 

data/lib/rbbt/workflow/step/run.rb

@@ -432,7 +432,7 @@ class Step
   end
 
   def abort
-    return if done? and status == :done
+    return if done? and (status == :done or status == :noinfo)
     _abort
     log(:aborted, "Job aborted") unless aborted? or error?
     self

data/share/Rlib/util.R

@@ -207,41 +207,6 @@ rbbt.acc <- function(data, new){
     }
 }
 
-rbbt.png_plot <- function(filename, width, height, p, ...){
-    png(filename=filename, width=width, height=height, ...);
-    eval(parse(text=p));
-}
-
-rbbt.heatmap <- function(filename, width, height, data, take_log=FALSE, ...){
-    opar = par()
-    png(filename=filename, width=width, height=height);
-
-    #par(cex.lab=0.5, cex=0.5, ...)
-
-    data = as.matrix(data)
-    data[is.nan(data)] = NA
-
-    #data = data[rowSums(!is.na(data))!=0, colSums(!is.na(data))!=0]
-    data = data[rowSums(is.na(data))==0, ]
-
-    if (take_log){
-        for (study in colnames(data)){
-            skip = sum(data[, study] <= 0) != 0
-            if (!skip){
-                data[, study] = log(data[, study])
-            }
-        }
-        data = data[, colSums(is.na(data))==0]
-    }
-
-    data = stdize(data)
-
-    heatmap.2(data, margins = c(20,5), scale='column')
-
-    dev.off();
-    par(opar)
-}
-
 rbbt.init <- function(data, new){
     if (is.null(data)){
         return(new);
@@ -303,73 +268,6 @@ rbbt.run <- function(filename){
 
 # UTILITIES
 
-# Addapted from http://www.phaget4.org/R/image_matrix.html
-rbbt.plot.matrix <- function(x, ...){
-    min <- min(x, na.rm=T);
-    max <- max(x, na.rm=T);
-    yLabels <- rownames(x);
-    xLabels <- colnames(x);
-    title <-c();
-# check for additional function arguments
-    if( length(list(...)) ){
-        Lst <- list(...);
-        if( !is.null(Lst$zlim) ){
-            min <- Lst$zlim[1];
-            max <- Lst$zlim[2];
-        }
-        if( !is.null(Lst$yLabels) ){
-            yLabels <- c(Lst$yLabels);
-        }
-        if( !is.null(Lst$xLabels) ){
-            xLabels <- c(Lst$xLabels);
-        }
-        if( !is.null(Lst$title) ){
-            title <- Lst$title;
-        }
-    }
-# check for null values
-    if( is.null(xLabels) ){
-        xLabels <- c(1:ncol(x));
-    }
-    if( is.null(yLabels) ){
-        yLabels <- c(1:nrow(x));
-    }
-
-    layout(matrix(data=c(1,2), nrow=1, ncol=2), widths=c(4,1), heights=c(1,1));
-
-# Red and green range from 0 to 1 while Blue ranges from 1 to 0
-    ColorRamp <- rgb( seq(0,1,length=256),  # Red
-                      seq(0,1,length=256),  # Green
-                      seq(1,0,length=256))  # Blue
-    ColorLevels <- seq(min, max, length=length(ColorRamp));
-
-# Reverse Y axis
-    reverse <- nrow(x) : 1;
-    yLabels <- yLabels[reverse];
-    x <- x[reverse,];
-
-# Data Map
-    par(mar = c(3,5,2.5,2));
-    image(1:length(xLabels), 1:length(yLabels), t(x), col=ColorRamp, xlab="",
-          ylab="", axes=FALSE, zlim=c(min,max));
-    if( !is.null(title) ){
-        title(main=title);
-    }
-    axis(BELOW<-1, at=1:length(xLabels), labels=xLabels, cex.axis=0.7);
-    axis(LEFT <-2, at=1:length(yLabels), labels=yLabels, las= HORIZONTAL<-1,
-         cex.axis=0.7);
-
-# Color Scale
-    par(mar = c(3,2.5,2.5,2));
-    image(1, ColorLevels,
-          matrix(data=ColorLevels, ncol=length(ColorLevels),nrow=1),
-          col=ColorRamp,
-          xlab="",ylab="",
-          xaxt="n");
-
-    layout(1);
-}
-
 rbbt.log <- function(m){
     head = "R-Rbbt"
     cat(paste(head, "> ", m,"\n",sep=""), file = stderr())
@@ -556,3 +454,162 @@ rbbt.get.modes <- function(x,bw = NULL,spar = NULL) {
     df2
 }
 
+#{{{ PLOTS
+
+rbbt.png_plot <- function(filename, width, height, p, ...){
+    png(filename=filename, width=width, height=height, ...);
+    eval(parse(text=p));
+}
+
+rbbt.heatmap <- function(filename, width, height, data, take_log=FALSE, ...){
+    opar = par()
+    png(filename=filename, width=width, height=height);
+
+    #par(cex.lab=0.5, cex=0.5, ...)
+
+    data = as.matrix(data)
+    data[is.nan(data)] = NA
+
+    #data = data[rowSums(!is.na(data))!=0, colSums(!is.na(data))!=0]
+    data = data[rowSums(is.na(data))==0, ]
+
+    if (take_log){
+        for (study in colnames(data)){
+            skip = sum(data[, study] <= 0) != 0
+            if (!skip){
+                data[, study] = log(data[, study])
+            }
+        }
+        data = data[, colSums(is.na(data))==0]
+    }
+
+    data = stdize(data)
+
+    heatmap.2(data, margins = c(20,5), scale='column')
+
+    dev.off();
+    par(opar)
+}
+
+# Addapted from http://www.phaget4.org/R/image_matrix.html
+rbbt.plot.matrix <- function(x, ...){
+    min <- min(x, na.rm=T);
+    max <- max(x, na.rm=T);
+    yLabels <- rownames(x);
+    xLabels <- colnames(x);
+    title <-c();
+# check for additional function arguments
+    if( length(list(...)) ){
+        Lst <- list(...);
+        if( !is.null(Lst$zlim) ){
+            min <- Lst$zlim[1];
+            max <- Lst$zlim[2];
+        }
+        if( !is.null(Lst$yLabels) ){
+            yLabels <- c(Lst$yLabels);
+        }
+        if( !is.null(Lst$xLabels) ){
+            xLabels <- c(Lst$xLabels);
+        }
+        if( !is.null(Lst$title) ){
+            title <- Lst$title;
+        }
+    }
+# check for null values
+    if( is.null(xLabels) ){
+        xLabels <- c(1:ncol(x));
+    }
+    if( is.null(yLabels) ){
+        yLabels <- c(1:nrow(x));
+    }
+
+    layout(matrix(data=c(1,2), nrow=1, ncol=2), widths=c(4,1), heights=c(1,1));
+
+# Red and green range from 0 to 1 while Blue ranges from 1 to 0
+    ColorRamp <- rgb( seq(0,1,length=256),  # Red
+                      seq(0,1,length=256),  # Green
+                      seq(1,0,length=256))  # Blue
+    ColorLevels <- seq(min, max, length=length(ColorRamp));
+
+# Reverse Y axis
+    reverse <- nrow(x) : 1;
+    yLabels <- yLabels[reverse];
+    x <- x[reverse,];
+
+# Data Map
+    par(mar = c(3,5,2.5,2));
+    image(1:length(xLabels), 1:length(yLabels), t(x), col=ColorRamp, xlab="",
+          ylab="", axes=FALSE, zlim=c(min,max));
+    if( !is.null(title) ){
+        title(main=title);
+    }
+    axis(BELOW<-1, at=1:length(xLabels), labels=xLabels, cex.axis=0.7);
+    axis(LEFT <-2, at=1:length(yLabels), labels=yLabels, las= HORIZONTAL<-1,
+         cex.axis=0.7);
+
+# Color Scale
+    par(mar = c(3,2.5,2.5,2));
+    image(1, ColorLevels,
+          matrix(data=ColorLevels, ncol=length(ColorLevels),nrow=1),
+          col=ColorRamp,
+          xlab="",ylab="",
+          xaxt="n");
+
+    layout(1);
+}
+
+# Adapted from: https://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html
+rbbt.plot.venn <- function(data, a, ...) {
+    library(VennDiagram)
+    group.matches <- function(data, fields) {
+        sub = data
+        for (i in 1:length(fields)) {
+            sub <- subset(sub, sub[,fields[i]] == T)
+        }
+        nrow(sub)
+    }
+
+    if (length(a) == 1) {
+        out <- draw.single.venn(group.matches(data, a), ...)
+    }
+    if (length(a) == 2) {
+        out <- draw.pairwise.venn(group.matches(data, a[1]), group.matches(data, a[2]), group.matches(data, a[1:2]), ...)
+    }
+    if (length(a) == 3) {
+        out <- draw.triple.venn(group.matches(data, a[1]), group.matches(data, a[2]), group.matches(data, a[3]), group.matches(data, a[1:2]), 
+            group.matches(data, a[2:3]), group.matches(data, a[c(1, 3)]), group.matches(data, a), ...)
+    }
+    if (length(a) == 4) {
+        out <- draw.quad.venn(group.matches(data, a[1]), group.matches(data, a[2]), group.matches(data, a[3]), group.matches(data, a[4]), 
+            group.matches(data, a[1:2]), group.matches(data, a[c(1, 3)]), group.matches(data, a[c(1, 4)]), group.matches(data, a[2:3]), 
+            group.matches(data, a[c(2, 4)]), group.matches(data, a[3:4]), group.matches(data, a[1:3]), group.matches(data, a[c(1, 2, 
+                4)]), group.matches(data, a[c(1, 3, 4)]), group.matches(data, a[2:4]), group.matches(data, a), ...)
+    }
+    if (length(a) == 5) {
+        out <- draw.quintuple.venn(
+            group.matches(data, a[1]), group.matches(data, a[2]), group.matches(data, a[3]), group.matches(data, a[4]), group.matches(data, a[5]), 
+            group.matches(data, a[c(1, 2)]), group.matches(data, a[c(1, 3)]), group.matches(data, a[c(1, 4)]), group.matches(data, a[c(1, 5)]), 
+            group.matches(data, a[c(2, 3)]), group.matches(data, a[c(2, 4)]), group.matches(data, a[c(2, 5)]),
+            group.matches(data, a[c(3, 4)]), group.matches(data, a[c(3, 5)]),
+            group.matches(data, a[c(4, 5)]),
+            group.matches(data, a[c(1, 2, 3)]),group.matches(data, a[c(1, 2, 4)]),group.matches(data, a[c(1, 2, 5)]),
+            group.matches(data, a[c(1, 3, 4)]),group.matches(data, a[c(1, 3, 5)]),
+            group.matches(data, a[c(1, 4, 5)]),
+            group.matches(data, a[c(2, 3, 4)]),group.matches(data, a[c(2, 3, 5)]),
+            group.matches(data, a[c(2, 4, 5)]),
+            group.matches(data, a[c(3, 4, 5)]),
+            group.matches(data, a[c(1, 2, 3, 4)]),group.matches(data, a[c(1, 2, 3, 5)]),group.matches(data, a[c(1, 2, 4, 5)]),group.matches(data, a[c(1, 3, 4, 5)]),group.matches(data, a[c(2, 3, 4, 5)]),
+            group.matches(data, a),
+            ...)
+
+    }
+    if (!exists("out")) 
+        out <- "Oops"
+    return(out)
+}
+
+
+rbbt.plot.text_scatter <- function(formula, data) {
+    plot(formula, data=data, cex = 0)
+    text(formula, data=data, cex = 0.6, labels=rownames(data))
+}

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.77
+  version: 5.21.78
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-03-06 00:00:00.000000000 Z
+date: 2017-04-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake