R/modules/user_manual/user_manualPanel.R

user.panel <-
  tabPanel("User Manual",
         navlistPanel("Table of contents", widths = c(3, 9),
                      tabPanel(tags$p(span(class='glyphicon glyphicon-list-alt')," About RPath"),
                               mainPanel(width = 12,
                                 wellPanel(
                                   h4("Getting started with RPath"),
                                   p("RPath is a shiny application for biologic pathway exploration.
                                     Shiny is an R package used to build web applications with R. A user opens the app on their browser, specifies a given set of inputs, these
                                     are transmitted to an R session where some code is evaluated and output is produced and transmitted
                                     back to the browser."),
                                   h4("Features"),
                                   p("RPath consists of 4 modules:"),
                                   tags$ul(
                                     tags$li(
                                       strong("Search module."),
                                       "Responsible for allowing the search of the biologic pathway through different data sources."
                                     ),
                                     tags$li(
                                       strong("Visualization module."),
                                       "Responsible for graphically representing the newtork."
                                     ),
                                     tags$li(
                                       strong("Data summarization (or analysis) module."),
                                       "Responsible for carrying out an analysis of the components of the route and showing the user its most characteristic elements."
                                     )
                                   ),
                                   h4("Version history"),
                                   tags$ul(
                                     tags$li(
                                       span(strong("v1.1."), em("May 2018.")),
                                       "Major version published on khaos.uma.es"
                                     ),
                                     tags$li(
                                       span(strong("v1.0."), em("Feb 2018.")),
                                       "First major version released on Github."
                                     )
                                   ),
                                   h4("Development team"),
                                   p("Active development team:"),
                                   tags$table(
                                     tags$tr(tags$th('Name'),tags$th('Email')),
                                     tags$tr(tags$td('Antonio Benitez Hidalgo'),tags$td('antonio.benitez@lcc.uma.es')),
                                     tags$tr(tags$td('Cesar Lobato Fernandez'),tags$td('ceslobfer95@uma.es')),
                                     class="table table-striped",
                                     width = 12
                                   ),
                                   p("Thanks to:"),
                                   tags$table(
                                     tags$tr(tags$th('Name'),tags$th('Email')),
                                     tags$tr(tags$td('Daniel Torres Ramirez'),tags$td('dantorram@uma.es')),
                                     tags$tr(tags$td('Maria Jose Munoz Gonzalez'),tags$td('marmungon@uma.es')),
                                     class="table table-striped",
                                     width=12
                                   ),
                                   img(src="http://khaos.uma.es/sites/default/files/banner_bg.jpg", class="img-responsive center-block manualR")
                                )
                               )
                      ),
                      tabPanel(tags$p(span(class='glyphicon glyphicon-search')," Search module"),
                               mainPanel(width = 12,
                                 wellPanel(
                                   h4("Searching on Pathway Commons"),
                                   p("RPath has a build-in search engine. We can perform searches across multiple databases
                                     using Pathway Commons' API (a member within the BioPAX community aimed at collecting biological pathway data represented in the BioPAX standard).
                                     Search term supports Lucene query syntax, making easy to search for pathways related to certain words."),
                                   p("For example, we can include the '?' or '*' characters to search for pathways whose name start with
                                     'gl' followed by a character + 'coly' followed by any word:"),
                                   img(src="img/usermanual/search_term_examples.PNG", class="img-responsive center-block manualR"),
                                   p("For more information about Lucene query syntax refer to the ",
                                     a("official documentation", href="https://lucene.apache.org/core/2_9_4/queryparsersyntax.html", target="_blank"),
                                     "."),
                                   p("In the Organism field we can type the organism on which we want to get the pathway for:"),
                                   img(src="img/usermanual/search_organism.PNG", class="img-responsive center-block manualR"),
                                   p("We can also specify on which database(s) we want to perform the search on (default is 'Reactome') along with
                                     the numbers of results we want to get:"),
                                   img(src="img/usermanual/search_data_source_num_search.PNG", class="img-responsive center-block manualR"),
                                   p("The results will be shown in a table:"),
                                   img(src="img/usermanual/search_results.PNG", class="img-responsive center-block manualR"),
                                   p("After selecting one row, you will be able to download the pathway in .OWL format (BioPAX standard) by pressing the button 'Download OWL'.")
                               ))
                      ),
                      tabPanel(tags$p(span(class='glyphicon glyphicon-list')," Data Summarization"),
                               mainPanel(width = 12,
                                 wellPanel(
                                   h4("Exploring the pathway"),
                                   p(class="alert alert-info", "Note that this panel is only accesible after selecting a pathway."),
                                   p("This module allow us to explore every single component of the pathway using SPARQL queries."),
                                   p("With SPARQL, we are able to query data stored in Pathway Commons without storing on our local machines using Pathway Commons' endpoint and
                                     perform complex queries which involves several databases."),
                                   img(src="img/usermanual/data_tabs.PNG", class="img-responsive center-block manualR"),
                                   p("On the first tab (", em("Summary"), ") we can download (or show) the Simple Interaction Format file (SIF) directly to our computer. It contains pairwise
                                     interactions between physical entities of our pathway. This format was first stablished by Cytoscape, a bioinformatics tool for pathway visualization
                                     so we can export the pathway and visualize it on third-party apps."),
                                   img(src="img/usermanual/data_tab_reactions.PNG", class="img-responsive center-block manualR"),
                                   p("On the second tab (", em("Example queries"), ") there are six different queries which gives information about, for example,
                                     the biochemical reactions that takes place on our pathway."),
                                   img(src="img/usermanual/data_example_bioreac.PNG", class="img-responsive center-block manualR"),
                                   p("The last tab (", em("Custom query"), ") allow scientists to compose their custom query. Note that the string '%s' will be replaced with the
                                     identifier (URI) of the selected pathway."),
                                   p(class="alert alert-info", "SPARQL query examples: http://bioqueries.uma.es/"),
                                   img(src="img/usermanual/data_custom_query.PNG", class="img-responsive center-block manualR")
                                 )
                               )
                      ),
                      tabPanel(tags$p(span(class='glyphicon glyphicon-picture')," Visualization"),
                               mainPanel(width = 12,
                                 wellPanel(
                                   h4("Pathway visualization"),
                                   p(class="alert alert-info", "Note that this panel is only accesible after selecting a pathway."),
                                   p("We can visualize the pathway as nodes and interactions only by transforming our pathway into Simple Interaction Format (SIF)."),
                                   img(src="img/usermanual/graph_binary_sif_graph.PNG", class="img-responsive center-block manualR"),
                                   h4("Type of relationships in a binary SIF file"),
                                   tags$table(
                                     tags$tr(
                                       tags$th('Name of interaction'),tags$th('Description'),tags$th('Image')),
                                     tags$tr(
                                       tags$td('In-complex-with'),
                                       tags$td('ComponentA is in complex with ComponentB. So, they are members og the same complex.'),
                                       tags$td(img(src="img/usermanual/graph_A_in_complex_with_B.PNG", class="img-responsive center-block manualR"))),
                                     tags$tr(
                                       tags$td('Interacts-with'),
                                       tags$td('ComponentA interacts with ComponentB. So, they are participants of the same interaction.'),
                                       tags$td(img(src="img/usermanual/graph_A_interacts_with_B.PNG", class="img-responsive center-block manualR"))),
                                     tags$tr(
                                       tags$td('Control-of-expression'),
                                       tags$td('ComponentA control the expression of ComponentB.'),
                                       tags$td(img(src="img/usermanual/graph_A_control_expression_of_B.PNG", class="img-responsive center-block manualR"))),
                                     tags$tr(
                                       tags$td('Control-of-fosforilation'),
                                       tags$td('ComponentA control the fosforilation of ComponentB.'),
                                       tags$td(img(src="img/usermanual/graph_A_control_of_fosforilation_of_B.PNG", class="img-responsive center-block manualR"))),
                                     tags$tr(
                                       tags$td('Control-state-change'),
                                       tags$td('ComponentA control the state change of ComponentB.'),
                                       tags$td(img(src="img/usermanual/graph_A_control_state_change_of_B.PNG", class="img-responsive center-block manualR"))),
                                     tags$tr(
                                       tags$td(p('Consumption-controlled-by'), p('Controls-production-of')),
                                       tags$td(p('The ComponentA (smallMolecule) is consumed by a reaction that is controled by a protein.'),
                                               p('The protein controls a reaction of which the ComponentA is an output.')),
                                       tags$td(img(src="img/usermanual/graph_A_two_relations_B_C_compuesto.PNG", class="img-responsive center-block manualR"))),
                                     tags$tr(
                                       tags$td('Chemical-affects'),
                                       tags$td('ComponentA (smallMolecule) has an effect on the ComponentB'),
                                       tags$td(img(src="img/usermanual/graph_A_chemical_affects_B.PNG", class="img-responsive center-block manualR"))),
                                     tags$tr(
                                       tags$td('Neighbor-of'),
                                       tags$td('ProteinA is neighbor of ProteinB and they are participants / controllers of same interaction.'),
                                       tags$td(img(src="img/usermanual/graph_A_neighbor_B.PNG", class="img-responsive center-block manualR"))),
                                     class="table table-hover",
                                     width=12
                                   ),
                                   h4("Extended graph"),
                                   p("As we said earlier, the binary SIF representation only contains pairwise interactions between physical
                                     entities. It's possible to visualize an extended graph representation of the pathway which contains complex relationships between entities."),
                                   img(src="img/usermanual/graph_extended_graph.PNG", class="img-responsive center-block manualR")
                                )
                              )
                            )
                      )
  )
benhid/Rpath documentation built on May 25, 2019, 3:22 p.m.