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fgcz / rawDiag

Brings Orbitrap mass spectrometry data to life; multi-platform, fast and colorful R package
https://bioconductor.org/packages/rawDiag
36 stars 11 forks source link

change default path reading files #36

Open cpanse opened 5 years ago

cpanse commented 5 years ago

brought up by Eduard

cpanse commented 5 years ago

consider having a rawDiagrc in $HOME containing a list of directories; has to be checked on the windows platform

cpanse commented 5 years ago
  1. download current rawDiag version

http://fgcz-ms.uzh.ch/~cpanse/rawDiag_0.0.18.tar.gz

  1. Set your Rprofile

the following snippet will configure the rawDiag shiny application that is searching into your download directory for raw files

cp@vpn-global-dhcp2-191:~ > cat .Rprofile 

rawDiagfilesystemRoot <- Sys.getenv('HOME')
rawDiagfilesystemDataDir = c("Downloads",
                        "data",
                        "raw"
  )
  1. check after restarting R
ls()

it should look like that:

screenshot 2018-10-25 at 13 29 48
  1. run the shiny application
library(shiny)
rawDiag_shiny <- system.file('shiny', 'bfabric_rawDiag', package = 'rawDiag')
shiny::runApp(rawDiag_shiny, display.mode = 'normal')
tobiasko commented 5 years ago

The requested URL /~cpanse/rawDiag_0.0.18.tar.gz was not found on this server.

tobiasko commented 5 years ago

tested for

sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS 10.13.6

locale: [1] C

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] ggplot2_2.2.1 base64enc_0.1-3 rmarkdown_1.9 tidyr_0.8.0 shiny_1.1.0 rawDiag_0.0.18 [7] protViz_0.3.1

loaded via a namespace (and not attached): [1] Rcpp_0.12.16 lubridate_1.7.3 lattice_0.20-35 assertthat_0.2.0 rprojroot_1.3-2 [6] digest_0.6.15 psych_1.8.3.3 mime_0.5 R6_2.2.2 cellranger_1.1.0 [11] plyr_1.8.4 backports_1.1.2 RSQLite_2.1.0 evaluate_0.10.1 httr_1.3.1
[16] pillar_1.2.1 rlang_0.2.0 lazyeval_0.2.1 readxl_1.0.0 rstudioapi_0.7
[21] hexbin_1.27.1 blob_1.1.1 readr_1.1.1 stringr_1.3.0 foreign_0.8-69
[26] bit_1.1-12 munsell_0.4.3 broom_0.4.4 httpuv_1.4.5 modelr_0.1.1
[31] pkgconfig_2.0.1 mnormt_1.5-5 htmltools_0.3.6 tibble_1.4.2 codetools_0.2-15 [36] crayon_1.3.4 dplyr_0.7.4 later_0.7.5 grid_3.3.2 nlme_3.1-130
[41] jsonlite_1.5 xtable_1.8-2 gtable_0.2.0 DBI_0.8 magrittr_1.5
[46] scales_0.5.0 stringi_1.1.7 reshape2_1.4.3 promises_1.0.1 bindrcpp_0.2.2
[51] tidyverse_1.2.1 xml2_1.2.0 tools_3.3.2 forcats_0.3.0 bit64_0.9-7
[56] glue_1.2.0 purrr_0.2.4 hms_0.4.2 yaml_2.1.18 colorspace_1.3-2 [61] rvest_0.3.2 memoise_1.1.0 knitr_1.20 bindr_0.1.1 haven_1.1.1

works!