Handle multiple files analyses in IFCshiny

gitdemont commented 2 years ago

IFCshiny (v <= 0.1.3) can be used to treat one file at a time.

The idea is to allow user to perform thier analyses on multiple files. Tasks to accomplish are:

[x] read multiple files
[x] apply gating strategy on multiple files
[x] navigate between files
[x] compare populations between files (graphs, ML, stats)
[x] export treated files
[x] export results (graphs, stats)

Others ? In dev branch for this can be installed by: -installing new dependencies (in addition to the one in IFCshiny readme:

install.packages(c("decido", "heatmaply"))

-installing IFCshiny with multiple files capability:

remotes::install_github(repo = "gitdemont/IFCshiny", ref = "batch", dependencies = FALSE)

HXB2AG commented 2 years ago

Apology for the late test, but not functional for me:

with install IFCshiny ref ="batch" -> version (0.1.2.100) (and IFC 0.1.2.101)

Avis dans if (.libPaths() %in% dirname(dirname(dirname(.rundir)))) .passphrase = "" : la condition a une longueur > 1 et seul le premier élément est utilisé Erreur dans get(x, envir = ns, inherits = FALSE) : objet 'convert_to_baseplot' introuvable

et IFCshiny 0.1.3

With the install of IFCshiny with the ref ="master" -> version 0.1.3 ((and IFC 0.1.2.101)

IFCshiny::runIFCshinyApp() Avis dans if (.libPaths() %in% dirname(dirname(dirname(.rundir)))) .passphrase = "" : la condition a une longueur > 1 et seul le premier élément est utilisé Erreur dans get(x, envir = ns, inherits = FALSE) : objet 'parseFCSname' introuvable

Thanks

gitdemont commented 2 years ago

Hi @HXB2AG,

Sorry for that. It happens because I did modifications in both IFC and IFCshiny dev versions. Making the batch branch of IFCshiny temporarily unavailable. I did plan to push things before but I was a little bit distracted by work engaged on plot rasterization to be able to handle millions of points in plot module of the app that I wanted to incorporate. But since IFCshiny is highly dependent on IFC, those kind of improvements require in-depth modifications of IFC internals in addition to IFCshiny itself.

Could you please try with the recent updates:

# remove former versions
try(remove.packages("IFC"))
try(remove.packages("IFCip"))
try(remove.packages("IFCshiny"))

# then in a fresh session
remotes::install_github(repo = "gitdemont/IFC", ref = "master", dependencies = FALSE, force = TRUE)
remotes::install_github(repo = "gitdemont/IFCip", ref = "master", dependencies = FALSE, force = TRUE)
remotes::install_github(repo = "gitdemont/IFCshiny", ref = "batch", dependencies = FALSE, force = TRUE)

# then once packages installed
IFCshiny::runIFCshinyApp()

HXB2AG commented 2 years ago

I have now a new problem, precisely with plot_rasterization ? : `IFCshiny::runIFCshinyApp()

Avis dans if (.libPaths() %in% dirname(dirname(dirname(.rundir)))) .passphrase = "" : la condition a une longueur > 1 et seul le premier élément est utilisé Erreur dans get(x, envir = ns, inherits = FALSE) : objet 'plot_raster' introuvable`

With IFC 0.1.2.102 IFCdata 0.0.1 IFCip 0.0.1 IFCshiny 0.1.2.102

gitdemont commented 2 years ago

This is quite weird. Just in case I bumped version of IFC@master to v0.1.2.103 and IFCshiny@batch to v0.1.2.103 So can you try

try(remove.packages("IFC"))
try(remove.packages("IFCshiny"))

# then in a fresh session
remotes::install_github(repo = "gitdemont/IFC", ref = "master", dependencies = FALSE, force = TRUE)
remotes::install_github(repo = "gitdemont/IFCshiny", ref = "batch", dependencies = FALSE, force = TRUE)

This should allow you to run

IFCshiny::runIFCshinyApp()

If it is not working could you tell me what are the results of

utils::packageVersion("IFC")
# expected: ‘0.1.2.103’
utils::packageVersion("IFCshiny")
# expected: ‘0.1.2.103’
try(invisible(getFromNamespace("plot_raster", "IFC")))
# expected: no error should be thrown

gitdemont commented 2 years ago

Batch branch has now been merged with master

gitdemont / IFCshiny

Handle multiple files analyses in IFCshiny #2