Permalink
Browse files

re-org into a package with runshinyGEO func and working on update_GEO…

…data
  • Loading branch information...
jasdumas committed Feb 1, 2017
1 parent dc426f2 commit b41e2bbf39dd5aa293532a49c682bfcd4b5734d3
Showing with 102 additions and 24 deletions.
  1. BIN .DS_Store
  2. BIN .RData
  3. +5 −0 .Rbuildignore
  4. +25 −0 .Rhistory
  5. +1 −1 .Rproj.user/E833DC/pcs/files-pane.pper
  6. +1 −1 .Rproj.user/E833DC/pcs/source-pane.pper
  7. +7 −7 .Rproj.user/E833DC/pcs/windowlayoutstate.pper
  8. +2 −2 .Rproj.user/E833DC/pcs/workbench-pane.pper
  9. +10 −0 .Rproj.user/E833DC/sdb/prop/INDEX
  10. +2 −0 .travis.yml
  11. +7 −7 DESCRIPTION
  12. +1 −0 NAMESPACE
  13. +14 −0 R/runshinyGEO.R
  14. +18 −0 R/update_GEOdata.R
  15. BIN { → inst/shiny-apps/shinyGEO}/RData/GSE13.RData
  16. BIN { → inst/shiny-apps/shinyGEO}/RData/GSE19915.RData
  17. 0 { → inst/shiny-apps/shinyGEO}/RData/getTestData.R
  18. 0 { → inst/shiny-apps/shinyGEO}/manifest.txt
  19. 0 { → inst/shiny-apps/shinyGEO}/misc/.Rapp.history
  20. 0 { → inst/shiny-apps/shinyGEO}/misc/addDeps.R
  21. 0 { → inst/shiny-apps/shinyGEO}/misc/bsModal.R
  22. 0 { → inst/shiny-apps/shinyGEO}/misc/html.R
  23. 0 { → inst/shiny-apps/shinyGEO}/misc/plot.shiny.km.R
  24. 0 { → inst/shiny-apps/shinyGEO}/misc/stripchart2.R
  25. 0 { → inst/shiny-apps/shinyGEO}/platforms/geo-platform-update.sh
  26. BIN { → inst/shiny-apps/shinyGEO}/platforms/platforms.RData
  27. 0 { → inst/shiny-apps/shinyGEO}/platforms/process-platforms.R
  28. +6 −6 { → inst/shiny-apps/shinyGEO}/series/geo-series-update.sh
  29. 0 { → inst/shiny-apps/shinyGEO}/series/process-series.R
  30. BIN { → inst/shiny-apps/shinyGEO}/series/series.RData
  31. 0 { → inst/shiny-apps/shinyGEO}/server.R
  32. 0 { → inst/shiny-apps/shinyGEO}/server/formatDE.R
  33. 0 { → inst/shiny-apps/shinyGEO}/server/server-clinical.R
  34. 0 { → inst/shiny-apps/shinyGEO}/server/server-io.R
  35. 0 { → inst/shiny-apps/shinyGEO}/server/server-merge.R
  36. 0 { → inst/shiny-apps/shinyGEO}/server/server-output.R
  37. 0 { → inst/shiny-apps/shinyGEO}/server/server-reactives.R
  38. 0 { → inst/shiny-apps/shinyGEO}/server/server-report.R
  39. 0 { → inst/shiny-apps/shinyGEO}/server/server-selection.R
  40. 0 { → inst/shiny-apps/shinyGEO}/server/server-survival.R
  41. 0 { → inst/shiny-apps/shinyGEO}/server/settings.R
  42. 0 { → inst/shiny-apps/shinyGEO}/ui.R
  43. 0 { → inst/shiny-apps/shinyGEO}/ui/ui.dashboard.body.R
  44. 0 { → inst/shiny-apps/shinyGEO}/ui/ui.dashboard.body.R~master
  45. 0 { → inst/shiny-apps/shinyGEO}/ui/ui.dashboard.header.R
  46. 0 { → inst/shiny-apps/shinyGEO}/ui/ui.dashboard.sidebar.R
  47. 0 { → inst/shiny-apps/shinyGEO}/ui/ui.tab.about.R
  48. 0 { → inst/shiny-apps/shinyGEO}/ui/ui.tab.analyses.R
  49. 0 { → inst/shiny-apps/shinyGEO}/ui/ui.tab.expression.R
  50. 0 { → inst/shiny-apps/shinyGEO}/ui/ui.tab.reproducible.R
  51. 0 { → inst/shiny-apps/shinyGEO}/www/AdminLTE/AdminLTE.css
  52. 0 { → inst/shiny-apps/shinyGEO}/www/AdminLTE/AdminLTE.min.css
  53. 0 { → inst/shiny-apps/shinyGEO}/www/AdminLTE/README-shiny-mods.md
  54. 0 { → inst/shiny-apps/shinyGEO}/www/AdminLTE/_all-skins.css
  55. 0 { → inst/shiny-apps/shinyGEO}/www/AdminLTE/_all-skins.min.css
  56. 0 { → inst/shiny-apps/shinyGEO}/www/AdminLTE/app.js
  57. 0 { → inst/shiny-apps/shinyGEO}/www/AdminLTE/app.min.js
  58. 0 { → inst/shiny-apps/shinyGEO}/www/AdminLTE/app.min.js.map
  59. BIN { → inst/shiny-apps/shinyGEO}/www/AdminLTE/fonts/Source_Sans_Pro_300.ttf
  60. BIN { → inst/shiny-apps/shinyGEO}/www/AdminLTE/fonts/Source_Sans_Pro_300italic.ttf
  61. BIN { → inst/shiny-apps/shinyGEO}/www/AdminLTE/fonts/Source_Sans_Pro_400.ttf
  62. BIN { → inst/shiny-apps/shinyGEO}/www/AdminLTE/fonts/Source_Sans_Pro_400italic.ttf
  63. BIN { → inst/shiny-apps/shinyGEO}/www/AdminLTE/fonts/Source_Sans_Pro_600.ttf
  64. BIN { → inst/shiny-apps/shinyGEO}/www/AdminLTE/fonts/Source_Sans_Pro_600italic.ttf
  65. BIN { → inst/shiny-apps/shinyGEO}/www/AdminLTE/fonts/Source_Sans_Pro_700.ttf
  66. 0 { → inst/shiny-apps/shinyGEO}/www/AdminLTE/h
  67. BIN { → inst/shiny-apps/shinyGEO}/www/PleaseWait.gif
  68. 0 { → inst/shiny-apps/shinyGEO}/www/bootstrap.css
  69. 0 { → inst/shiny-apps/shinyGEO}/www/ecsu.css
  70. 0 { → inst/shiny-apps/shinyGEO}/www/ecsu.js
  71. BIN misc/.DS_Store
  72. +3 −0 shinyGEO.Rproj
  73. BIN www/.DS_Store
  74. BIN www/AdminLTE/.DS_Store
View
BIN -2 KB (75%) .DS_Store
Binary file not shown.
View
BIN +8.15 KB (110%) .RData
Binary file not shown.
View
@@ -1,2 +1,7 @@
^.*\.Rproj$
^\.Rproj\.user$
^1200x592\.png$
^jasmine_dumas_user2016_poster_update\.pdf$
^jasmine_dumas_user2016_poster_update\.pptx$
^jasmine_dumas_user2016_poster\.pptx$
^\.travis\.yml$
View
@@ -278,3 +278,28 @@ library(shiny)
runApp()
library(shinydashboard)
runApp()
library(devtools)
devtools::document()
devtools::document()
devtools::use_build_ignore(c("1200x592.png", "jasmine_dumas_user2016_poster_update.pdf", ))
devtools::use_build_ignore(c("1200x592.png", "jasmine_dumas_user2016_poster_update.pdf", "jasmine_dumas_user2016_poster_update.pptx", "jasmine_dumas_user2016_poster.pptx"))
use_build_ignore(".travis.yml")
cat("Platforms updated .../n")
cat("Platforms updated ...\n")
?source
source("inst/shiny-apps/shinyGEO/platforms/geo-platform-update.sh")
?system
?load
system("inst/shiny-apps/shinyGEO/platforms/geo-platform-update.sh", intern=T)
system("inst/shiny-apps/shinyGEO/platforms/geo-platform-update.sh", intern=F)
system("inst/shiny-apps/shinyGEO/series/geo-series-update.sh")
install.packages("httr")
install.packages("httr")
library(httr)
data <- httr::GET("https://www.ncbi.nlm.nih.gov/geo/browse/")
data
system("echo "Update GEO data..."
data=$(curl --silent "https://www.ncbi.nlm.nih.gov/geo/browse/" | grep "total_count")
")
system("inst/shiny-apps/shinyGEO/series/geo-series-update.sh")
q()
@@ -1,5 +1,5 @@
{
"path" : "~/Desktop/R-directory/shinyGEO",
"path" : "~/Desktop/R-directory/shinyGEO/inst/shiny-apps/shinyGEO/series",
"sortOrder" : [
{
"ascending" : true,
@@ -1,3 +1,3 @@
{
"activeTab" : -1
"activeTab" : 2
}
@@ -1,14 +1,14 @@
{
"left" : {
"panelheight" : 648,
"splitterpos" : 172,
"topwindowstate" : "HIDE",
"windowheight" : 686
"panelheight" : 588,
"splitterpos" : 221,
"topwindowstate" : "NORMAL",
"windowheight" : 626
},
"right" : {
"panelheight" : 648,
"splitterpos" : 410,
"panelheight" : 588,
"splitterpos" : 359,
"topwindowstate" : "NORMAL",
"windowheight" : 686
"windowheight" : 626
}
}
@@ -1,6 +1,6 @@
{
"TabSet1" : 1,
"TabSet2" : 2,
"TabSet1" : 0,
"TabSet2" : 0,
"TabZoom" : {
}
}
@@ -1,4 +1,14 @@
~%2FDesktop%2FR-directory%2Fggplotly_example_shinyGEO.R="AC55ADC2"
~%2FDesktop%2FR-directory%2FshinyGEO%2F.Rbuildignore="A691ADBC"
~%2FDesktop%2FR-directory%2FshinyGEO%2F.travis.yml="D7222D2C"
~%2FDesktop%2FR-directory%2FshinyGEO%2FDESCRIPTION="4B1B4EBC"
~%2FDesktop%2FR-directory%2FshinyGEO%2FR%2FrunshinyGEO.R="CA6D5AF5"
~%2FDesktop%2FR-directory%2FshinyGEO%2FR%2Fupdate_GEOdata.R="BB659C7A"
~%2FDesktop%2FR-directory%2FshinyGEO%2FREADME.md="A79A8A41"
~%2FDesktop%2FR-directory%2FshinyGEO%2Finst%2Fshiny-apps%2FshinyGEO%2Fplatforms%2Fprocess-platforms.R="4AC31A7"
~%2FDesktop%2FR-directory%2FshinyGEO%2Finst%2Fshiny-apps%2FshinyGEO%2Fseries%2Fgeo-series-update.sh="B6CD553C"
~%2FDesktop%2FR-directory%2FshinyGEO%2Finst%2Fshiny-apps%2FshinyGEO%2Fseries%2Fprocess-series.R="9F73B3AE"
~%2FDesktop%2FR-directory%2FshinyGEO%2Finst%2Fshiny-apps%2FshinyGEO%2Fui.R="456798E4"
~%2FDesktop%2FR-directory%2FshinyGEO%2Fmisc%2FaddDeps.R="7B964844"
~%2FDesktop%2FR-directory%2FshinyGEO%2Fmisc%2Fstripchart2.R="923533EC"
~%2FDesktop%2FR-directory%2FshinyGEO%2Fserver%2Fserver-clinical.R="3FECE0DB"
View
@@ -0,0 +1,2 @@
language: R
cache: packages
View
@@ -1,9 +1,10 @@
Package: shinyGEO
Title: Gene Expression Omnibus Analysis with Shiny
Version: 0.0.0.9000
Version: 1.0.0
Authors@R: c(
person("Jasmine", "Dumas", email = "jasmine.dumas@gmail.com", role = c("aut", "cre")),
person("Garrett", "Dancik", email = "dancikg@easternct.edu", role = "aut"),
person("Michael", "Gargano", role = "ctb"),
person("Ken-Heng Henry", "Liao", role = "ctb"),
person("Branden", "Spratt", role = "ctb"),
person("Greg", "Harper", role = "ctb"))
@@ -13,21 +14,20 @@ Description: A web application to download, parse, transform, model,
across genes, probes and phenotype groups. A report with code
and can also be generated for complete reporducibility at the console.
Depends: R (>= 3.2.0)
BugReports: https://github.com/jasdumas/shinyGEO/issues
URL: https://github.com/jasdumas/shinyGEO
BugReports: https://github.com/gdancik/shinyGEO/issues
URL: http://gdancik.github.io/shinyGEO/
Imports:
shiny,
GEOquery,
Biobase,
reshape2,
survival,
affy,
limma,
affy,
shinyBS,
GGally,
ggplot2,
shinyAce,
knitr,
DT,
Suggests:
License: MIT + file LICENSE
DT
License: MIT + file LICENSE.txt
View
@@ -0,0 +1 @@
exportPattern("^[[:alpha:]]+")
View
@@ -0,0 +1,14 @@
#' Run shinyGEO application
#'
#' @return Nothing is returned except a shiny app launched locally showing
#' shinyGEO.
#' @examples \dontrun{ runshinyGEO() }
#' @export
runshinyGEO <- function() {
appDir <- system.file("shiny-apps", "shinyGEO", package = "shinyGEO")
if (appDir == "") {
stop("Could not find apps directory. Try re-installing `shinyGEO`.", call. = FALSE)
}
shiny::runApp(appDir, display.mode = "normal")
}
View
@@ -0,0 +1,18 @@
#' Update series and platform data from GEO
#'
#' @return Series and platform data are updated from the Gene Expression
#' Omnibus and stored as R data objects.
#'
#' @examples \dontrun{ update_GEOdata() }
#' @export
update_GEOdata <- function(){
# platform update
system("inst/shiny-apps/shinyGEO/platforms/geo-platform-update.sh")
source("inst/shiny-apps/shinyGEO/platforms/process-platforms.R")
cat("Platforms data updated ...\n")
# series update
system("inst/shiny-apps/shinyGEO/series/geo-series-update.sh")
source("inst/shiny-apps/shinyGEO/series/process-series.R")
cat("Series data updated")
}
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
@@ -3,14 +3,14 @@
DIR=/home/user
{
mv $DIR/series.csv $DIR/backup-series.csv &&
echo "Backup created.."
} || {
echo "No local series data found.. one will be created"
}
}
echo "Update GEO data..."
data=$(curl --silent "https://www.ncbi.nlm.nih.gov/geo/browse/" | grep "total_count")
@@ -26,10 +26,10 @@ if [ "$i != 1" ]
then
wget --content-disposition "https://www.ncbi.nlm.nih.gov/geo/browse/?view=series&zsort=date&mode=csv&page=$i&display=5000" -q -O ->> $DIR/series.csv
else
wget --content-disposition "https://www.ncbi.nlm.nih.gov/geo/browse/?view=series&zsort=date&mode=csv&page=$i&display=5000" -q -a ->> $DIR/series.csv
wget --content-disposition "https://www.ncbi.nlm.nih.gov/geo/browse/?view=series&zsort=date&mode=csv&page=$i&display=5000" -q -a ->> $DIR/series.csv
fi
done
done
echo "Finished update...data saved to -> series.csv"
echo "Finished update...data saved to -> series.csv"
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
View
BIN -6 KB misc/.DS_Store
Binary file not shown.
View
@@ -12,6 +12,9 @@ Encoding: UTF-8
RnwWeave: knitr
LaTeX: pdfLaTeX
AutoAppendNewline: Yes
StripTrailingWhitespace: Yes
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
View
BIN -6 KB www/.DS_Store
Binary file not shown.
View
Binary file not shown.

0 comments on commit b41e2bb

Please sign in to comment.