From 305be2b24043442fd3988a32a73bab7c23ef18fa Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Thu, 14 Aug 2014 10:29:14 +0200
Subject: [PATCH] cont. new r utils
---
R/core_commons.R | 103 +++++++++++++++++++++++++++++++++++-----
R/datatable_utils.R | 2 +-
R/df_utils.R | 77 ------------------------------
R/ggplot/ggplot_utils.R | 1 +
4 files changed, 92 insertions(+), 91 deletions(-)
delete mode 100644 R/df_utils.R
diff --git a/R/core_commons.R b/R/core_commons.R
index fa8937b..0e95ac1 100644
--- a/R/core_commons.R
+++ b/R/core_commons.R
@@ -20,35 +20,37 @@ require.auto <- function(x){
}
}
+#qlibrary <- function(libname) {library(as.character(substitute(libname)), quietly=T, warn.conflicts=F, character.only=T )}
+
+## set a default cran r mirror
+#cat(".Rprofile: Setting Goettingen repository\n")
+r = getOption("repos") # hard code the UK repo for CRAN

+r["CRAN"] = "http://ftp5.gwdg.de/pub/misc/cran/"
+options(repos = r)
+rm(r)
+
+
+## load core packages
require.auto(plyr)
require.auto(stringr)
require.auto(reshape2)
#require.auto(reshape2, quietly=T, warn.conflicts=F)
-require.auto(scales)
+## load on purpose after plyr
require.auto(dplyr)
-
#require.auto(data.table)
+## user browser for help
options(help_type="html")
+
+## plot more characters per line
options(width=150)
# for sqldf to avoid the use of tckl
options(gsubfn.engine = "R")
-##### set the r mirror
-#cat(".Rprofile: Setting Goettingen repository\n")
-r = getOption("repos") # hard code the UK repo for CRAN

-r["CRAN"] = "http://ftp5.gwdg.de/pub/misc/cran/"
-options(repos = r)
-rm(r)
-
-
-
-
-#qlibrary <- function(libname) {library(as.character(substitute(libname)), quietly=T, warn.conflicts=F, character.only=T )}
@@ -77,6 +79,81 @@ unlen <- function(x) length(unique(x))
pp <- function(dat) page(dat, method = "print")
+########################################################################################################################
+#### data.frame manipulation
+
+subsample <- function(df, sampleSize, ...){
+ df[sample(1:nrow(df), min(sampleSize, nrow(df)), ...),]
+}
+
+shuffle <- function(df) df[sample(nrow(df)),]
+
+first <- function(x, n=1) head(x,n)
+
+as.df <- function(dt) as.data.frame(dt)
+
+
+
+rownames2column <- function(df, colname){
+ df <- as.df(df)
+ df$tttt <- rownames(df);
+ rownames(df) <- NULL;
+ rename(df, c(tttt=colname))
+}
+
+
+column2rownames<- function(df, colname){
+#browser()
+ rownames(df) <- ac(df[,colname])
+ df[colname] <- NULL
+ return(df)
+}
+
+## pushing some columns to the right end of a data.frame
+push_right <- function(df, pushColNames){
+ df[,c(setdiff(names(df),pushColNames), pushColNames)]
+}
+
+
+push_left <- function(df, pushColNames){
+ df[,c(pushColNames, setdiff(names(df),pushColNames))]
+}
+
+
+set_names <- function(df, newnames){
+ df<- as.df(df)
+ names(df) <- newnames;
+ return(df)
+}
+
+
+print_head <- function(df, desc=NULL){
+ print(head(df))
+ return(df)
+}
+
+
+fac2char <- function(mydata, convert=names(mydata)[sapply(mydata, is.factor)]){
+ if(length(convert)==0)
+ return(mydata)
+
+ inputColOrder <- names(mydata)
+
+ convertData <- subset(mydata, select= names(mydata)%in%convert)
+ convertData <- as.data.frame(lapply(convertData, as.character), stringsAsFactors = FALSE)
+
+ keepData <- subset(mydata, select=!(names(mydata)%in%convert))
+ newdata <- cbind(convertData, keepData)
+ newdata <- newdata[,inputColOrder]
+
+ return(newdata)
+}
+
+
+## workaround for biomart
+## Deprecated: load dplyr after biomart to avoid this problem
+#dselect <- function(...) dplyr::select(...)
+
########################################################################################################################
#### File System
diff --git a/R/datatable_utils.R b/R/datatable_utils.R
index 3a7733d..7b9214d 100644
--- a/R/datatable_utils.R
+++ b/R/datatable_utils.R
@@ -1,4 +1,4 @@
- require.auto(data.table)
+require.auto(data.table)
dt.merge <- function(dfA, dfB, by=intersect(names(dfA), names(dfB)) , ...) {
diff --git a/R/df_utils.R b/R/df_utils.R
deleted file mode 100644
index 1bf549a..0000000
--- a/R/df_utils.R
+++ /dev/null
@@ -1,77 +0,0 @@
-
-
-subsample <- function(df, sampleSize, ...){
- df[sample(1:nrow(df), min(sampleSize, nrow(df)), ...),]
-}
-
-shuffle <- function(df) df[sample(nrow(df)),]
-
-first <- function(x, n=1) head(x,n)
-
-as.df <- function(dt) as.data.frame(dt)
-
-
-## small wrappers
-
-
-
-
-rownames2column <- function(df, colname){
- df <- as.df(df)
- df$tttt <- rownames(df);
- rownames(df) <- NULL;
- rename(df, c(tttt=colname))
-}
-
-column2rownames<- function(df, colname){
-#browser()
- rownames(df) <- ac(df[,colname])
- df[colname] <- NULL
- return(df)
-}
-
-## pushing some columns to the right end of a data.frame
-push_right <- function(df, pushColNames){
- df[,c(setdiff(names(df),pushColNames), pushColNames)]
-}
-
-push_left <- function(df, pushColNames){
- df[,c(pushColNames, setdiff(names(df),pushColNames))]
-}
-
-set_names <- function(df, newnames){
- df<- as.df(df)
- names(df) <- newnames;
- return(df)
-}
-
-
-## dplyr utilities
-
-print_head <- function(df, desc=NULL){
- print(head(df))
- return(df)
-}
-
-
-fac2char <- function(mydata, convert=names(mydata)[sapply(mydata, is.factor)]){
- if(length(convert)==0)
- return(mydata)
-
- inputColOrder <- names(mydata)
-
- convertData <- subset(mydata, select= names(mydata)%in%convert)
- convertData <- as.data.frame(lapply(convertData, as.character), stringsAsFactors = FALSE)
-
- keepData <- subset(mydata, select=!(names(mydata)%in%convert))
- newdata <- cbind(convertData, keepData)
- newdata <- newdata[,inputColOrder]
-
- return(newdata)
-}
-
-
-## workaround for biomart
-dselect <- function(...) dplyr::select(...)
-
-
diff --git a/R/ggplot/ggplot_utils.R b/R/ggplot/ggplot_utils.R
index b77ae14..e613b24 100644
--- a/R/ggplot/ggplot_utils.R
+++ b/R/ggplot/ggplot_utils.R
@@ -1,5 +1,6 @@
require.auto(ggplot2)
+require.auto(scales)
--
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