# Gene-Expression-Plots prototype Manual ## Disclaimer Note that the Application is a prototype. It is not stable, as some necessary things are missing like validations, Error-handling, etc.. ## Usage ### Terminology Imagine you want to plot gene expression counts resulting from a heat shock experiment carried out on your model organism of choice, e.g. witch plants. - **Group**: represents a collection of samples for a specific experimental condition, e.g. apical meristem exposed to heat shock for ten minutes. A group has one or more samples: - **Sample**: represents a collection of replicates within a group, e.g. tissue sample obtained after zero days, three, and five days after exposure to the heat shock, respectively. A sample has one or more replicates: - **Replicate**: typical for RNA-Seq experiments is the requirement of biological replicates in order to obtain robustness of results against noise. A 'replicate' thus is a single measurement of RNA-Seq counts from a respective tissue sample. Each replicate has a single count table as produced by the typical RNA-Seq analysis pipelines (e.g. Kallisto or Salmon). _Note: All groups, samples, and replicates must have the same gene gene accession identifiers._ ### Uploading Data Data upload is done in the *Data* Tab of the app. There are 2 different ways of uploading your data to the application. #### From replicate-tables See above terminology for details on 'replicate tables'. - In the _Data_ page, click the _plus_ icon and fill out the presented form. - The form represents the upload of either a single replicate file, or many replicates that belong to a specific sample within a specific group. - When uploading several replicates at once, make sure the table parameters match. - When uploading replicates for an existing group and sample, make sure the group and sample names match, otherwise a new group or sample will be created. - Each uploaded Group will appear on the main _Data_ page. Further replicate uploads to an existing group will update its _sample_ and _replicates_ count. _Note: it is recommended to export the uploaded data, so that it can be reimported more easily in the future._ #### From existing json source This basically is picking up plotting after having saved a previous 'project'. Load exported data and continue plotting. - Access the menu via the right Side-Drawer (grey bar at the right of your browser window) in the *Data* page. - Here you can either import previously exported data or directly export your processed data (from replicate-tables - see below) to JSON. - Once the import is done, you can see your data in the respective list. ### Plotting #### Create an expression plot for a gene - Switch to the *Plots* page and open the side-drawer on the right. - Choose a gene by its accessionId. You can search by typing in the input field. _Be aware that *for now* only the first 10 matches are displayed in the drop-down._ - Optionally select whether to show the legend using the _showlegend_ checkbox. - Once you hit **SAVE** a bar plot for the chosen gene is displayed. - Hovering the mouse over a plot will show a _modebar_ with various controls (e.g. export plot to a PNG file). #### Add another plot You can compare gene expression by putting side by side expression bar-plots. Just repeat the process for creating a plot this time selecting the other gene identifier. _Note: The **RESET** button has no functionality yet. Make sure to export your data for quick reimporting and replotting._ ## Current Issues - **WARNING**: Do not reload the page. Your data will be lost. - For now there is no way to edit or delete data and plots. If you make a mistake in the upload form, you have to reload the page and go again. - There are no validations for your input tables. Make sure they are in the correct format. - Manual navigation using the URL bar is not correctly configured.