Commit f466500a authored by Holger Brandl's avatar Holger Brandl

replaced all occurences of require.auto with require_auto

parent b1dab5fc
#library(BiocGenerics, quietly=T, warn.conflicts=F ) #library(BiocGenerics, quietly=T, warn.conflicts=F )
#library(Biostrings, quietly=T) #library(Biostrings, quietly=T)
#require.auto(BiocGenerics )x #require_auto(BiocGenerics )x
require.auto(Biostrings) require_auto(Biostrings)
read.fasta <- function(fileName){ read.fasta <- function(fileName){
......
...@@ -217,7 +217,7 @@ DEF_DAVID_ONTOLOGIES=ontologies=c("GOTERM_CC_FAT", "GOTERM_MF_FAT", "GOTERM_BP_F ...@@ -217,7 +217,7 @@ DEF_DAVID_ONTOLOGIES=ontologies=c("GOTERM_CC_FAT", "GOTERM_MF_FAT", "GOTERM_BP_F
davidAnnotationChart <- function( someGenes, ontologies=DEF_DAVID_ONTOLOGIES ){ davidAnnotationChart <- function( someGenes, ontologies=DEF_DAVID_ONTOLOGIES ){
require.auto(RDAVIDWebService) ## just works if installed on non-network-drive (e.g. /tmp/) require_auto(RDAVIDWebService) ## just works if installed on non-network-drive (e.g. /tmp/)
## expexted to have a column with gene_id ## expexted to have a column with gene_id
# echo("processing list with", length(someGenes), "genes") # echo("processing list with", length(someGenes), "genes")
......
...@@ -22,8 +22,8 @@ options(gsubfn.engine = "R") ...@@ -22,8 +22,8 @@ options(gsubfn.engine = "R")
## automatic package installation ## automatic package installation
## @Deprecated use require_auto instead ## @Deprecated use require_auto instead
require.auto <- function(x){ require_auto <- function(x){
warning("require.auto is deprecated. Use require_auto instead") warning("require_auto is deprecated. Use require_auto instead")
x <- as.character(substitute(x)) x <- as.character(substitute(x))
......
require.auto(data.table) require_auto(data.table)
dt.merge <- function(dfA, dfB, by=intersect(names(dfA), names(dfB)) , ...) { dt.merge <- function(dfA, dfB, by=intersect(names(dfA), names(dfB)) , ...) {
......
...@@ -2,8 +2,8 @@ ...@@ -2,8 +2,8 @@
#library(ggplot2) #library(ggplot2)
#library(reshape2) #library(reshape2)
require.auto(ggdendro) require_auto(ggdendro)
require.auto(grid) require_auto(grid)
## Adopted from http://cwcode.wordpress.com/2013/01/30/ggheatmap-version-2/ ## Adopted from http://cwcode.wordpress.com/2013/01/30/ggheatmap-version-2/
...@@ -164,7 +164,7 @@ ggheatmap <- function(x, rowlabels=T, xshift=ifelse(rowlabels, 10, 0), xcompress ...@@ -164,7 +164,7 @@ ggheatmap <- function(x, rowlabels=T, xshift=ifelse(rowlabels, 10, 0), xcompress
if(F){ #### DEBUG if(F){ #### DEBUG
require.auto(mvtnorm) require_auto(mvtnorm)
sigma=matrix(0,10,10) sigma=matrix(0,10,10)
sigma[1:4,1:4] <- 0.6 sigma[1:4,1:4] <- 0.6
sigma[6:10,6:10] <- 0.8 sigma[6:10,6:10] <- 0.8
......
require.auto(ggplot2) require_auto(ggplot2)
require.auto(scales) require_auto(scales)
require.auto(grid) require_auto(grid)
scale_fill_redgreed <- function() scale_fill_manual(values = c("red","darkgreen")) scale_fill_redgreed <- function() scale_fill_manual(values = c("red","darkgreen"))
...@@ -157,7 +157,7 @@ plotPDF <- function(fileBaseName, expr, ...){ pdf(paste0(fileBaseName, ".pdf"), ...@@ -157,7 +157,7 @@ plotPDF <- function(fileBaseName, expr, ...){ pdf(paste0(fileBaseName, ".pdf"),
## create a custom color palette for a fixed set of values ## create a custom color palette for a fixed set of values
## scale_fill_manual(values = create_palette(unique(csWithTopoT1$t1_type)), drop = FALSE) ## scale_fill_manual(values = create_palette(unique(csWithTopoT1$t1_type)), drop = FALSE)
create_palette <- function(x, pal = 'Set1'){ create_palette <- function(x, pal = 'Set1'){
require.auto(RColorBrewer) require_auto(RColorBrewer)
ux <- sort(unique(x)) ux <- sort(unique(x))
n <-length(ux) n <-length(ux)
......
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