man/mk_combine_file.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mk_combine_file}
-\alias{mk_combine_file}
-\title{Combine RMB Settings With Different Collisional Energies}
-\usage{
-mk_combine_file(sett_fns, fname)
-}
-\arguments{
-\item{sett_fns}{A list of settings files.}
-
-\item{fname}{The name of the combined file.}
-}
-\value{
-fname
-}
-\description{
-Combine the RMB settings files
-}
-\details{
-Combine RMB settings with different collisional energies into one
-settings file with multiple collisional energy entries.
-}
-\author{
-Todor Kondić
-}

man/mk_sett_file.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{mk_sett_file}
-\alias{mk_sett_file}
-\title{Generate RMassBank settings file.}
-\usage{
-mk_sett_file(sett_alist, file)
-}
-\arguments{
-\item{sett_alist}{The named list of settings that are different
-from the RMassBank defaults.}
-
-\item{file}{The name of the YAML specification that will be merged
-with the template Rmb settings file.}
-}
-\description{
-Produce the Rmb Settings file
-}
-\details{
-Produce the Rmb Settings file based on the customisation file in
-YAML format.
-}

man/no_drama_mkdir.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{no_drama_mkdir}
-\alias{no_drama_mkdir}
-\title{Create directories without drama}
-\usage{
-no_drama_mkdir(path)
-}
-\arguments{
-\item{path}{Names of the directories.}
-}
-\value{
-The character string containing the input argument \code{path}.
-}
-\description{
-Create directories without drama.
-}
-\details{
-Create directories without drama.
-}
-\author{
-Todor Kondić
-}

man/presc.do.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/run.R
-\name{presc.do}
-\alias{presc.do}
-\title{Prescreening on bunch of files.}
-\usage{
-presc.do(fn_data, fn_cmpd_l, mode, dest = ".", proc = F, ...)
-}
-\arguments{
-\item{fn_data}{The mzML files. Basis for the out directory name
-generation.}
-
-\item{fn_cmpd_l}{The compound list.}
-
-\item{mode}{RMB mode.}
-
-\item{dest}{Destination directory.}
-
-\item{proc}{Amount of processors, or FALSE.}
-
-\item{fn_cmpd_list}{The compound list CSV.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Do the prescreening.
-}
-\author{
-Todor Kondić
-}

man/presc.plot.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.plot}
-\alias{presc.plot}
-\title{Plot the Output of Prescreen}
-\usage{
-presc.plot(prescdf, mode, out = "prescreen.pdf", fn_cmpd_l,
-  pal = "Dark2", cex = 0.75, rt_digits = 2, m_digits = 4)
-}
-\arguments{
-\item{prescdf}{File table data-frame. See presc.shiny for details.}
-
-\item{mode}{RMB mode.}
-
-\item{out}{The name of the output file.}
-
-\item{fn_cmpd_l}{The compound list name.}
-
-\item{pal}{ColorBrewer palette name.}
-
-\item{cex}{As in legend.}
-
-\item{rt_digits}{Number of digits after the point for the retention time.}
-
-\item{m_digits}{Number of digits after the point for the mass.}
-
-\item{wd}{Sequence of data dirs containing the prescreen subdir.}
-
-\item{digits}{Number of significant digits for peak ret times.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Plot the output of prescreen.
-}
-\author{
-Todor Kondić
-
-Mira Narayanan
-
-Anjana Elapavalore
-}

man/presc.shiny.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{presc.shiny}
-\alias{presc.shiny}
-\title{Prescreening with Shiny}
-\usage{
-presc.shiny(prescdf, mode, fn_cmpd_l, pal = "Dark2", cex = 0.75,
-  rt_digits = 2, m_digits = 4)
-}
-\arguments{
-\item{prescdf}{File table data-frame. Columns: Files,ID,wd,tag,set_name ...}
-
-\item{mode}{RMassBank mode.}
-
-\item{fn_cmpd_l}{Compound list file name.}
-
-\item{pal}{ColorBrewer palette.}
-
-\item{cex}{Size of fonts.}
-
-\item{rt_digits}{Number of decimal places for the retention time.}
-
-\item{m_digits}{Number of decimal places for the mass.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Prescreening using shiny interface.
-}
-\author{
-Jessy Krier
-
-Mira Narayanan
-
-Hiba Mohammed Taha
-
-Anjana Elapavalore
-
-Todor Kondić
-}

man/rendersmiles2.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{rendersmiles2}
-\alias{rendersmiles2}
-\title{Turn SMILES to an Image Using Online Resource}
-\usage{
-rendersmiles2(smiles, style = "cow", ...)
-}
-\arguments{
-\item{smiles}{The SMILES string.}
-
-\item{style}{Structure style.}
-
-\item{...}{Hand over to renderurl.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Render smiles from an online resource.
-}
-\author{
-Todor Kondić
-}

man/renderurl.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mix.R
-\name{renderurl}
-\alias{renderurl}
-\title{Render Compound from an Online Resource}
-\usage{
-renderurl(depictURL, coords = c(0, 0, 100, 100),
-  filename = tempfile(fileext = ".svg"))
-}
-\arguments{
-\item{depictURL}{The URL of the object to plot.}
-
-\item{coords}{The positioning of the image (in data coords).}
-
-\item{filename}{Temp filename.}
-}
-\value{
-Nothing useful.
-}
-\description{
-Helper function for rendersmiles2
-}
-\author{
-Todor Kondić
-}

shiny-lessons.org

+#+TITLE: Empirical Notes on Shiny 
+
+
+- It used to be better for Shinyscreen to retain the bare minimum of
+  observers and keep as much of functionality as possible inside
+  reactive functions. The fluidity of UI experience was reported to be
+  better. Probably the logic of the application got better, too. But,
+  going full reactive can sometimes be exhausting. These days, we
+  build some stuff inside observers. All in moderation, though.
+
+- Assignment to a reactive value does not add a dependency on that
+  value.
+
+- A reactive values list is not adding a dependency on all its
+  members. Not even if it was nested inside some other reactive values
+  list.
+
+- An ordinary list inside reactive values list, if used, will add
+  dependency on all its members. Even if only some of its members are
+  used, the dependency is on all the members.
+
+- Recursive dependencies can get ugly. If really needed, do not
+  depend, but use isolate.
+
+- Do *NOT* change the value of things you depend on. This creates
+  infinite loops. It may even work, but will be sloooow.
+
+- Single output produced by any input from a group of inputs: separate
+  observers are needed do differentiate between which of the inputs
+  have been triggered.
+
+- The only way to detect if the button press was acted upon in a
+  reactive expression that depends on multiple inputs is to raise a
+  flag, or write the state of the button when done.
+
+- As development progresses, keep an observer that transforms
+  shinyscreen mess into the logics of the workflow. Then move out as
+  much of this as possible into reactive functions. Example,
+  Shinyscreen underlying script flow was first emulated by an
+  observer.