diff --git a/README.md b/README.md index ac6bae0..cc81252 100644 --- a/README.md +++ b/README.md @@ -284,4 +284,49 @@ 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') +```