Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
bioinfo
datautils
Commits
f466500a
Commit
f466500a
authored
Nov 03, 2015
by
Holger Brandl
Browse files
replaced all occurences of require.auto with require_auto
parent
b1dab5fc
Changes
6
Hide whitespace changes
Inline
Side-by-side
R/bio/bioinfo_commons.R
View file @
f466500a
#library(BiocGenerics, quietly=T, warn.conflicts=F )
#library(Biostrings, quietly=T)
#require
.
auto(BiocGenerics )x
#require
_
auto(BiocGenerics )x
require
.
auto
(
Biostrings
)
require
_
auto
(
Biostrings
)
read.fasta
<-
function
(
fileName
){
...
...
R/bio/diffex_commons.R
View file @
f466500a
...
...
@@ -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
){
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
# echo("processing list with", length(someGenes), "genes")
...
...
R/core_commons.R
View file @
f466500a
...
...
@@ -22,8 +22,8 @@ options(gsubfn.engine = "R")
## automatic package installation
## @Deprecated use require_auto instead
require
.
auto
<-
function
(
x
){
warning
(
"require
.
auto is deprecated. Use require_auto instead"
)
require
_
auto
<-
function
(
x
){
warning
(
"require
_
auto is deprecated. Use require_auto instead"
)
x
<-
as.character
(
substitute
(
x
))
...
...
R/datatable_commons.R
View file @
f466500a
require
.
auto
(
data.table
)
require
_
auto
(
data.table
)
dt.merge
<-
function
(
dfA
,
dfB
,
by
=
intersect
(
names
(
dfA
),
names
(
dfB
))
,
...
)
{
...
...
R/ggplot/ggheatmap.R
View file @
f466500a
...
...
@@ -2,8 +2,8 @@
#library(ggplot2)
#library(reshape2)
require
.
auto
(
ggdendro
)
require
.
auto
(
grid
)
require
_
auto
(
ggdendro
)
require
_
auto
(
grid
)
## 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
if
(
F
){
#### DEBUG
require
.
auto
(
mvtnorm
)
require
_
auto
(
mvtnorm
)
sigma
=
matrix
(
0
,
10
,
10
)
sigma
[
1
:
4
,
1
:
4
]
<-
0.6
sigma
[
6
:
10
,
6
:
10
]
<-
0.8
...
...
R/ggplot_commons.R
View file @
f466500a
require
.
auto
(
ggplot2
)
require
.
auto
(
scales
)
require
.
auto
(
grid
)
require
_
auto
(
ggplot2
)
require
_
auto
(
scales
)
require
_
auto
(
grid
)
scale_fill_redgreed
<-
function
()
scale_fill_manual
(
values
=
c
(
"red"
,
"darkgreen"
))
...
...
@@ -157,7 +157,7 @@ plotPDF <- function(fileBaseName, expr, ...){ pdf(paste0(fileBaseName, ".pdf"),
## create a custom color palette for a fixed set of values
## scale_fill_manual(values = create_palette(unique(csWithTopoT1$t1_type)), drop = FALSE)
create_palette
<-
function
(
x
,
pal
=
'Set1'
){
require
.
auto
(
RColorBrewer
)
require
_
auto
(
RColorBrewer
)
ux
<-
sort
(
unique
(
x
))
n
<-
length
(
ux
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment