helpPage.R

helpPage = function(){
    wellPanel(h3('Using NeuroExpresso.org'),
              p('This application aims to facilitate visualization of the data contained in the 
                                                      NeuroExpresso database. The images show screenshots of the application
                                                      with numbered annotations. Here we explain what each part of the application
                                                      do, referencing them with the number they are marked with'),
              img(src = 'annotated.png',width = '100%'),
              h4('1. Select Gene'),
              p('Write the official symbol of the gene of interest. If a gene that is not included in the
                data is entered, suggestions will appear under the box ("Did you mean:..."). If what you enter is a synonym for
                an official symbol, you will also see suggestions (Synonym of:...). This section also gives a link to Allen Institute
                mouse ISH data for the gene.'),
              h4('2. Select Region'),
              fluidRow(
                  column(6, 
                         p('Select brain region of interest. Selecting a brain region will display cell types isolated from said brain region.
                                                                 Astrocytes and oligodendrocytes are exceptions to this. Since we were unable to find expression data from region
                                                                 specific glial cells yet we knew they were prevelant throughout the brain, they were added to all brain regions
                                                                 unless there is a region specific alternative (Bergmann glia replaces astrocytes in Cerebellum). Note that some 
                                                                 regions are subsets of each other.')
                  ),
                  column(6,shinyTree('staticRegionTree'))
              ),
              h4('3. Select Platform'),
              p('The data included in NeuroExpresso compiled from multiple independent studies. It includes data generated using ',
                a(href="http://www.chibi.ubc.ca/Gemma/arrays/showArrayDesign.html?id=7",target= '_blank', 'GPL339'),
                ' and ',
                a(href="http://www.chibi.ubc.ca/Gemma/arrays/showArrayDesign.html?id=3",target= '_blank' ,'GPL1261'),
                ' microarray chips along with single cell RNA-seq data generated by ',
                a(href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585",target= '_blank' ,'Tasic et al.'),
                'The genes included in the GPL339 platform is a subset of genes included in GPL1261, while RNA-seq data from
                Tasic et al. provides the highest covarage of genes. Choosing GPL339 will show expression in all samples included
                in NeuroExpresso. Choosing GPL1261 will include samples generated using GPL1261 and RNA-seq data by Tasic et al.,
                while increasing the genes avaiable for query. Finally Choosing RNAseq will only show RNA-seq data while making all
                genes detected in the dataset available for querying. If a gene you entered is available in a larger platform, you will
                recieve a notification below the "Select Gene" box'),
              h4('4. Select hierachy'),
              p('This option allows to choose if you want to split samples by cell types or different studies. Implented as a way to detect
                study specific biases'),
              h4('5. Tree selection'),
              p('This shows the hierarchical tree specified by "Select Hiearchy" box. By checking the boxes you can control which samples
                 do you want to display or how do you want to group them together in the hierarchy (eg. checking neurons will add a neuron group
                 to the plot, including all neuronal subtypes).'),
              h4('6. Options'),
              p('These options allow you to customize the plot and get additional information. Fixed axis option makes the axis ranges constant
                between all plots to allow easier comparison of expression values between genes. Color option removes cell type colors from samples.
                "Is marker?" option shows if the gene you are looking at was identified as a marker gene based on our study.'),
              h4('7. Display'),
              p('Use if you not want to display Microarray and RNA-seq data together. Note that RNA-seq data in this visualization is normalized
                to be on the scale of microarray data. To get the real expression values, please refer to the original data source.'),
              h4('8. The plot'),
              p('The plot shows expression of all samples (in the case of RNA-seq data clusters) for the choosen gene. You can get more information
                about a particular sample by clicking on the points. The plot can be resized from the bottom-right corner and an image can be downloaded
                using the gear icon on the upper-right corner.'),
              h4('9. Differential expression'),
              p('This tab allows you to assign samples into two groups to run a basic differential expression analysis. You pick samples by drawing
                a box around them on the plot and clicking to "Save group" button. If no samples are selected when the button is pressed, all samples
                on display are assigned to the group so you can use other sample filtering methods to pick your samples.'),
              h4('10. Help page'),
              p('You are here.'),
              h4('Sharing with query strings'),
              p('You can share links to specific genes using query strings. Gene, region and platform boxes can be filled this way.'),
              a(href="http://neuroexpresso.org/?gene=Eno2&region=Midbrain&platform=GPL1261",target= '_blank' ,'http://neuroexpresso.org/?gene=Eno2&region=Midbrain&platform=GPL1261')
              )

}