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bioinfo
ngs_tools
Commits
43b8e6fb
Commit
43b8e6fb
authored
Apr 24, 2017
by
Holger Brandl
Browse files
fixed missing slice model table
parent
f864e445
Changes
1
Hide whitespace changes
Inline
Side-by-side
common/cp_enrichment.R
View file @
43b8e6fb
...
...
@@ -20,10 +20,10 @@ Options:
opts
<-
docopt
(
doc
,
commandArgs
(
TRUE
))
## does not work when spining
# opts <- docopt(doc, "--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast" )
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.3
6
/R/core_commons.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.3
6
/R/ggplot_commons.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.3
6
/R/bio/cp_utils.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.3
6
/R/bio/diffex_commons.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.3
8
/R/core_commons.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.3
8
/R/ggplot_commons.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.3
8
/R/bio/cp_utils.R"
)
devtools
::
source_url
(
"https://raw.githubusercontent.com/holgerbrandl/datautils/v1.3
8
/R/bio/diffex_commons.R"
)
load_pack
(
knitr
)
load_pack
(
DT
)
...
...
@@ -317,10 +317,14 @@ walk(term_barplot_files$file, function(pngFile){ cat(paste0("<img src='", pngFil
keggPathways
<-
enrResults
%>%
filter
(
ontology
==
"kegg"
)
%$%
ac
(
ID
)
%>%
unique
()
# %>% head(3) ## todo remove debug head
# results='asis'
#
# #+
results='asis'
, echo=FALSE
if
(
!
exists
(
"keggPathways"
)
||
length
(
keggPathways
)
==
0
){
cat
(
"No enriched pathways found"
)
}
else
{
return
()
quit
()
}
load_pack
(
naturalsort
)
...
...
@@ -351,7 +355,8 @@ sliceData <- overlayData %>% rify_names() %>% select_(., .dots=naturalsort(ac(na
#sliceData %>% head %>% kable()
data.frame
(
set
=
names
(
sliceData
))
%>%
mutate
(
slice_index
=
row_number
())
%>%
kable
()
data.frame
(
set
=
names
(
sliceData
))
%>%
mutate
(
slice_index
=
row_number
())
%>%
knitr
::
kable
()
pwPlotDir
<-
".pathways"
...
...
@@ -469,7 +474,7 @@ makeTooltip <- function(entrez_id){
##
#+ results="asis", echo=FALSE
#+ results="asis", echo=FALSE
## simple non-clickable plots
## http://stackoverflow.com/questions/12588323/r-how-to-extract-values-for-the-same-named-elements-across-multiple-objects-of
...
...
@@ -540,7 +545,7 @@ pathwayPlots %>% plyr::l_ply(createImgMap)
## respin it for cild inclusion
# require(knitr); setwd("/Volumes/projects/bioinfo/scripts/ngs_tools/dev/common"); spin("cp_enrichment.R", knit=F)
}
#
}
#' ## Notes
#' Other interesting tools to perform enrichment testing
...
...
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