From noreply at r-forge.r-project.org  Sun Dec 15 00:56:57 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun, 15 Dec 2013 00:56:57 +0100 (CET)
Subject: [CHNOSZ-commits] r59 - in pkg/CHNOSZ: . R inst
Message-ID: <20131214235657.8F07B186A7F@r-forge.r-project.org>

Author: jedick
Date: 2013-12-15 00:56:57 +0100 (Sun, 15 Dec 2013)
New Revision: 59

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/read.expr.R
   pkg/CHNOSZ/R/revisit.R
   pkg/CHNOSZ/R/util.fasta.R
   pkg/CHNOSZ/inst/NEWS
Log:
read.expr() allows multiple filters; read.fasta() gets protein name before first space in header line


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2013-11-24 22:13:51 UTC (rev 58)
+++ pkg/CHNOSZ/DESCRIPTION	2013-12-14 23:56:57 UTC (rev 59)
@@ -1,6 +1,6 @@
-Date: 2013-11-24
+Date: 2013-12-15
 Package: CHNOSZ
-Version: 1.0.2
+Version: 1.0.2-1
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey M. Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/read.expr.R
===================================================================
--- pkg/CHNOSZ/R/read.expr.R	2013-11-24 22:13:51 UTC (rev 58)
+++ pkg/CHNOSZ/R/read.expr.R	2013-12-14 23:56:57 UTC (rev 59)
@@ -88,9 +88,9 @@
   edata <- edata[!ina, ]
   # apply a filter if requested
   if(!is.null(filter)) {
-    jfilter <- match(names(filter), colnames(edata))
-    ifilter <- grep(filter[[1]], edata[, jfilter])
-    edata <- edata[ifilter, ]
+    ifilter <- 1:nrow(edata)
+    for(i in 1:length(filter)) ifilter <- intersect(ifilter, grep(filter[[i]], edata[, names(filter)[[i]]]))
+    edata <- edata[unique(ifilter), ]
   }
   # that should be it
   protein <- edata[, iid]

Modified: pkg/CHNOSZ/R/revisit.R
===================================================================
--- pkg/CHNOSZ/R/revisit.R	2013-11-24 22:13:51 UTC (rev 58)
+++ pkg/CHNOSZ/R/revisit.R	2013-12-14 23:56:57 UTC (rev 59)
@@ -163,6 +163,8 @@
         # plot the points for a referenced objective
         ylab <- "loga1"
         xlab <- "loga2"
+        if(is.null(xlim)) xlim <- extendrange(loga2)
+        if(is.null(ylim)) ylim <- extendrange(loga1)
         plot(loga2, loga1, xlab=xlab, ylab=ylab, pch=pch, col=col, xlim=xlim, ylim=ylim)
         # add a 1:1 line
         lines(range(loga2), range(loga2), col="grey")

Modified: pkg/CHNOSZ/R/util.fasta.R
===================================================================
--- pkg/CHNOSZ/R/util.fasta.R	2013-11-24 22:13:51 UTC (rev 58)
+++ pkg/CHNOSZ/R/util.fasta.R	2013-12-14 23:56:57 UTC (rev 59)
@@ -107,7 +107,7 @@
   bnf <- strsplit(basename(file),split=".",fixed=TRUE)[[1]][1]
   organism <- bnf
   # protein/gene name is from header line for entry
-  # (strip the ">" and go to the first space or underscore)
+  # (strip the ">" and go to the first space)
   if(is.null(id)) id <- as.character(palply(1:length(i), function(j) {
     # get the text of the line
     f1 <- linefun(i[j],i[j])
@@ -118,9 +118,7 @@
     # discard the leading '>'
     f2 <- substr(f1, 2, nchar(f1))
     # keep everything before the first space
-    f3 <- strsplit(f2," ")[[1]][1]
-    # then before or after the first underscore
-    return(strsplit(f3,"_")[[1]][1])
+    return(strsplit(f2," ")[[1]][1])
   } ))
   if(ret=="count") {
     counts <- count.aa(sequences, start, stop, type)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2013-11-24 22:13:51 UTC (rev 58)
+++ pkg/CHNOSZ/inst/NEWS	2013-12-14 23:56:57 UTC (rev 59)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.2 (2013-11-24)
+CHANGES IN CHNOSZ 1.0.2-1 (2013-12-15)
 --------------------------------------
 
 - Updated extdata/protein/Sce.csv.xz using Saccharomyces Genome Database
@@ -13,6 +13,9 @@
 - read.fasta() gets new argument 'id'; when supplied, it skips reading
   the protein names from the FASTA headers.
 
+- When reading protein names from the FASTA headers, read.fasta() stops
+  only at the first space, not space or underscore as before.
+
 - info() no longer specially sets state of "O2" or "oxygen" to gas.
 
 - In thermo$obigt, names of gases (e.g. "oxygen") are used only for the
@@ -20,7 +23,11 @@
   63-79. Both gases and aqueous species can continue to be referenced by
   their chemical formula.
 
+- In read.expr(), allow multiple filter specifications.
 
+- In revisit(), extend ranges of axes of scatter plots.
+
+
 CHANGES IN CHNOSZ 1.0.1 (2013-07-04)
 ------------------------------------