Update README.md

fgcz · Jul 27, 2022 · 01fac47 · 01fac47
1 parent d49439d
commit 01fac47
Showing 1 changed file with 50 additions and 51 deletions.
diff --git a/README.md b/README.md
@@ -1,14 +1,60 @@
 ![](https://github.com/fgcz/bfabric/workflows/R-CMD-check-bfabric/badge.svg)
 
-# bfabric R package
+# bfabricShiny R package
 
-enables connecting R and bfabric using REST
+## Demonstration
 
+1. enables connecting R and bfabric using REST
 
 ![bfabricPy-read-R](https://user-images.githubusercontent.com/4901987/65041207-7c757c80-d956-11e9-90ca-9c3e2e0ca724.gif)
 
+2. command line triggered analytics
 
-# INSTALL
+![code_snippet_demo](https://user-images.githubusercontent.com/4901987/181242377-a9bf3988-b193-494c-91c9-a010500ee3f2.gif)
+
+```{r}
+## R --no-save < code_snippet.R
+## devtools::install_github("fgcz/bfabricShiny")
+## devtools::install_github("fgcz/rawDiag")
+stopifnot(R.Version()['major'] >= '4',
+    require('rawDiag'),
+    require('bfabricShiny'))
+
+## Define B-Fabric input workunit
+workunitid <- 165473
+
+## Query metadata from B-Fabric
+Q <- bfabricShiny::read(login, webservicepassword,
+  endpoint = 'resource',
+  query = list('workunitid' = workunitid), as_data_frame=FALSE)
+
+## setting root directory
+rawfilenames <- Q$res |>
+    sapply(function(x)file.path('/srv/www/htdocs/', x$relativepath))
+
+## Extract MS data from BLOBs using the rawDiag R package
+## That requires storage access via SSH, NFS, or SAMBA
+RAW <- rawfilenames |>
+    parallel::mclapply(rawDiag::read.raw, mc.cores = 12) |>
+    base::Reduce(f = rbind)
+
+## Print a summary
+RAW |> rawDiag::summary.rawDiag()
+
+## Have fun with visualization https://doi.org/10.1021/acs.jproteome.8b00173
+## (a)
+RAW |> rawDiag::PlotPrecursorHeatmap(bins = 25)
+## (b)
+RAW |> rawDiag::PlotPrecursorHeatmap(bins = 25) +
+  ggplot2::facet_wrap(~ filename)
+## (c)
+RAW |> rawDiag::PlotTicBasepeak(method = 'overlay')
+## (d)
+RAW |> rawDiag::PlotInjectionTime(method = 'overlay')
+```
+
+
+## INSTALL
 
 ```{bash}
 apt-get install r-base libcurl4-openssl-dev 
@@ -28,8 +74,7 @@ devtools::install_github('fgcz/bfabricShiny', build_vignettes = FALSE, quiet = F
 ```
 
 
-# Demonstration
-
+# Use cases
 
 ## Run shiny based queue generator application
 
@@ -284,49 +329,3 @@ The idea is to fetch a RData file stored in bfabric.
 
 
 
-## Command Line Triggered Visual Exploration
-
-
-![code_snippet_demo](https://user-images.githubusercontent.com/4901987/181242377-a9bf3988-b193-494c-91c9-a010500ee3f2.gif)
-
-
-```{r}
-## R --no-save < code_snippet.R
-## devtools::install_github("fgcz/bfabricShiny")
-## devtools::install_github("fgcz/rawDiag")
-stopifnot(R.Version()['major'] >= '4',
-    require('rawDiag'),
-    require('bfabricShiny'))
-
-## Define B-Fabric input workunit
-workunitid <- 165473
-
-## Query metadata from B-Fabric
-Q <- bfabricShiny::read(login, webservicepassword,
-  endpoint = 'resource',
-  query = list('workunitid' = workunitid), as_data_frame=FALSE)
-
-## setting root directory
-rawfilenames <- Q$res |>
-    sapply(function(x)file.path('/srv/www/htdocs/', x$relativepath))
-
-## Extract MS data from BLOBs using the rawDiag R package
-## That requires storage access via SSH, NFS, or SAMBA
-RAW <- rawfilenames |>
-    parallel::mclapply(rawDiag::read.raw, mc.cores = 12) |>
-    base::Reduce(f = rbind)
-
-## Print a summary
-RAW |> rawDiag::summary.rawDiag()
-
-## Have fun with visualization https://doi.org/10.1021/acs.jproteome.8b00173
-## (a)
-RAW |> rawDiag::PlotPrecursorHeatmap(bins = 25)
-## (b)
-RAW |> rawDiag::PlotPrecursorHeatmap(bins = 25) +
-  ggplot2::facet_wrap(~ filename)
-## (c)
-RAW |> rawDiag::PlotTicBasepeak(method = 'overlay')
-## (d)
-RAW |> rawDiag::PlotInjectionTime(method = 'overlay')
-```