isoverse/isoviewer

graphical user interface components for exploring isotope data

isoverse

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isoviewer's Issues

show package version information on the welcome page

zoom filtering for continuous flow plots

add zoom filtering for continuous flow plots using the time_interval and zoom parameters of the plotting function

add mouseover information on plots

provide mouseover information on plots, especially if vendor data table is provided
probably best with a separate "info" box that displays the datasets and datapoints neaerst to the mouse cursor

allow adding of user defined ratios

add a "add ratio" button that adds user defined ratios (simple set of numeric enter boxes?) to the trace selection (also make the auto-detection of ratios better or get rid of it altogether?)

careful about reload of the whole selector with changing isofile selection - use only "masses" from the table to check whether they're the same or have changed with different isofile selection

GUI state - download settings + variables as file / restore from file

• in the server version, allow folks to download the GUI state (settings and select variables) so they can re-upload to the server at a later point and resume where they left off

re-reading collections from outdated isoreader versions

if this can happen automatically on application start, it would be convenient but very slow and without feedback to the user. probably better to implement it in such a way that if someone uses a collection inside the app that has outdated isofiles, ask whether they want to re-read the collection (re-read collection is always an option next to the dropdown and asks whether people want to change read paramters)

allow for direct launch of a dataset

if iso_files parameter is provided and is a single file, should show a simplified GUI that has only the name of the dataset at the top as the only tab besides the "info" and "close". with the symbol of dual inlet vs. cont. flow vs. scan, plus some useful information about the dataset (number of files, maybe size of the object)

implement iso_start_monitor

have a simple navbar with "isomonitor", "welcome", name of the data folder to be monitored (with # of data files in it), and the close button

Goal: allow an easy way to monitor the data off the mass spec in real time. Make it possible to host this server on the mass spec itself and then just point to it from the remote (same as for iso_start_viewer)

Features:

• show the navbar with all the folders passed to the function (or make a sub menu of subfolders if those are available? or one menu item with the whole folder and one with the subfolders? ) or maybe an easy function to provide a list of folders and subfolders? i.e. list( folder1 = list_folders('folder'), folder2 = list_folders('folder2'), etc. - what if there are too many folders in a submenu? is it possible to scroll submenues? another possibility is just to put the whole folder structure into the navbar (for each provided folder) with multiple submenus if (include_sub_folders = TRUE), maybe that's the easiest...
• have a refresh button in the GUI taskbar that checks for new files in that folder (NOT the subfolders, those must be selected explicitly in the menu) and automatically pulls them into the files list (and have them automatically selected). Note: best combine this with the possibility to allow for single select mode in the file selector table so it's possible to click on individual files and have the auto zoom from auto-plot-refresh activated and just click through all chromatograms this way
• show in the code preview that the path is simply the folder name
• have a checkbox forauto-refresh plot (which could be useful in the general viewer as well? for folks who want to have GUI selections including zoom window automatically translate to the plot)
• make us of the not-yet-implemented "iso_plot_data()" tab for plotting data in the vendor data table live (with automatic plot refresh upon refreshing the iso files from the folder)

Isoviewer crashes when selecting empty data files

UW_DI_O2 <- iso_read_dual_inlet("data_raw/UW_IsoLab_DualInlet_O2")
isoviewer::iso_start_viewer()

the UW_DI_O2 data set has several "empty" data files at the end. If one of these is selected the viewer app immediately crashes and cannot be reopened without restarting R or closing and reopening the project.

select_files in code generation is missing iso_ prefix

disable auto-refresh

picking out individual mass/ratios with automatic reload is too slow for larger datasets. Instead have an "Apply" button as well and use "please select at least one mass/ratio and click the apply button" as the error message

allow sorting of masses and ratios

allow sorting - this is easy on the isoreader side but should also be possible in the GUI

save relative paths instead of absolute

in the isofiles read on a server it would be useful to save the file path relative to the data root in the file_info$file_path instead of the full path. This will allow re-reading data files even if the root changes.

prereqs for implementation:
isoverse/isoreader#1
isoverse/isoreader#10

Error during install of Isoviewer

Installation of isoviewer from Github according to the instructions fails with "Error in eval(exprs[i], envir) : object '%OR%' not found"
R version is 4.1.0, devtools and rtools are installed, isoreader and isoprocessor all installed OK.
Any ideas?
Best wishes,
Simon

deal with unread/unavailable data

deal properly with unread/unavailable data when aggregating (info box? part of problems?)

upgrade dataset download

• instead of straight up download, provide a modal dialog that asks whether to download the entire dataset or the _subset version
• provide choice of downloading as rds, excel or feather (i.e. replace the former download tab)
• include code chunks for the download once the button has been clicked (store in settings so this is automatically included on reload)

info tables - "select all" leads to double trigger of reactive downstream

this can be slow when it double triggers plot or large data tables to refresh, probably somewhere in viewer_module_selector_rable