[CHNOSZ-commits] r509 - in pkg/CHNOSZ: . R inst inst/extdata/refseq man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Oct 19 12:33:10 CEST 2019
Author: jedick
Date: 2019-10-19 12:33:10 +0200 (Sat, 19 Oct 2019)
New Revision: 509
Removed:
pkg/CHNOSZ/inst/extdata/refseq/protein_refseq.csv.xz
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/protein.info.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
remove protein_refseq.csv.xz
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-10-19 06:22:14 UTC (rev 508)
+++ pkg/CHNOSZ/DESCRIPTION 2019-10-19 10:33:10 UTC (rev 509)
@@ -1,6 +1,6 @@
Date: 2019-10-19
Package: CHNOSZ
-Version: 1.3.3-5
+Version: 1.3.3-6
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2019-10-19 06:22:14 UTC (rev 508)
+++ pkg/CHNOSZ/R/examples.R 2019-10-19 10:33:10 UTC (rev 509)
@@ -28,7 +28,7 @@
}
demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density",
- "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "glycinate",
+ "ORP", "findit", "ionize", "buffer", "protbuff", "glycinate",
"mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite", "wjd",
"bugstab", "Shh", "saturation", "adenine", "DEW", "lambda", "TCA", "aluminum", "bison", "AkDi"), save.png=FALSE) {
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2019-10-19 06:22:14 UTC (rev 508)
+++ pkg/CHNOSZ/inst/NEWS 2019-10-19 10:33:10 UTC (rev 509)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.3-5 (2019-10-19)
+CHANGES IN CHNOSZ 1.3.3-6 (2019-10-19)
--------------------------------------
- describe.reaction(): revert the change of using a double arrow. The
@@ -17,6 +17,9 @@
associated files. The data files and functions have been moved to the
JMDplots package (https://github.com/jedick/JMDplots).
+- Remove protein_refseq.csv.xz, which has been moved to
+ protein_refseq61.csv in JMDplots.
+
CHANGES IN CHNOSZ 1.3.3 (2019-08-02)
------------------------------------
Deleted: pkg/CHNOSZ/inst/extdata/refseq/protein_refseq.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2019-10-19 06:22:14 UTC (rev 508)
+++ pkg/CHNOSZ/man/extdata.Rd 2019-10-19 10:33:10 UTC (rev 509)
@@ -76,7 +76,7 @@
\item \code{mkfaa.sh} Combine the contents of .faa.gz files into a single FASTA file (to use e.g. for making a BLAST database).
\item \code{protein.refseq.R} Calculate average amino acid composition of all proteins for each organism identified by a taxonomic ID.
\item \code{trim_refseq.R} Keep only selected organism names (reduces number of taxa from 6758 to 779, helps to control package size).
- \item \code{protein_refseq.csv.xz} Output from above. See example in \code{\link{pinfo}}.
+ \item \code{protein_refseq.csv.xz} Output from above. NOTE: This file has been moved to \code{protein_refseq61.csv.xz} (\url{https://github.com/jedick/JMDplots}).
\item \code{taxid.names.R} Generate a table of scientific names for the provided taxids. Requires the complete \code{names.dmp} and \code{nodes.dmp} from NCBI taxonomy files.
\item \code{taxid_names.csv.xz} Output from above.
NOTE: For backward compatibility with the example BLAST files for the Bison Pool metagenome, the packaged file merges records for taxids found in either RefSeq 57 or 61.
Modified: pkg/CHNOSZ/man/protein.info.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.info.Rd 2019-10-19 06:22:14 UTC (rev 508)
+++ pkg/CHNOSZ/man/protein.info.Rd 2019-10-19 10:33:10 UTC (rev 509)
@@ -114,36 +114,6 @@
protein.formula(pinfo("P53_PIG"))
protein.formula(pinfo(pinfo("P53_PIG")))
-## using protein.formula: average oxidation state of
-## carbon of proteins from different organisms (Dick, 2014)
-# get amino acid compositions of microbial proteins
-# generated from the RefSeq database
-file <- system.file("extdata/refseq/protein_refseq.csv.xz", package="CHNOSZ")
-ip <- add.protein(read.csv(file, as.is=TRUE))
-# only use those organisms with a certain
-# number of sequenced bases
-ip <- ip[as.numeric(thermo()$protein$abbrv[ip]) > 50000]
-pf <- protein.formula(thermo()$protein[ip, ])
-zc <- ZC(pf)
-# the organism names we search for
-# "" matches all organisms
-terms <- c("Natr", "Halo", "Rhodo", "Acido", "Methylo",
- "Chloro", "Nitro", "Desulfo", "Geo", "Methano",
- "Thermo", "Pyro", "Sulfo", "Buchner", "")
-tps <- thermo()$protein$ref[ip]
-plot(0, 0, xlim=c(1, 15), ylim=c(-0.3, -0.05), pch="",
- ylab=expression(italic(Z)[C]),
- xlab="", xaxt="n", mar=c(6, 3, 1, 1))
-for(i in 1:length(terms)) {
- it <- grep(terms[i], tps)
- zct <- zc[it]
- points(jitter(rep(i, length(zct))), zct, pch=20)
-}
-terms[15] <- paste("all", length(ip))
-axis(1, 1:15, terms, las=2)
-title(main=paste("Average oxidation state of carbon in proteins",
- "by taxID in NCBI RefSeq (after Dick, 2014)", sep="\n"))
-
\dontshow{opar <- par(no.readonly=TRUE)}
# using pinfo() with regexp=TRUE:
# plot ZC and nH2O/residue of HOX proteins
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2019-10-19 06:22:14 UTC (rev 508)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2019-10-19 10:33:10 UTC (rev 509)
@@ -1511,9 +1511,9 @@
NOTE: It may be more convenient to do this with functions and data that have been moved to the [JMDplots](https://github.com/jedick/JMDplots) package:
```{r JMDplots, eval = FALSE}
-y <- yeastgfp("ER.to.Golgi")
+y <- JMDplots::yeastgfp("ER.to.Golgi")
ina <- is.na(y$abundance)
-aa <- yeast.aa(y$protein[!ina])
+aa <- JMDplots::yeast.aa(y$protein[!ina])
ip <- add.protein(aa)
```
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