Introduction
This article explains the data processing blocks that you can add to the experiment map. It assumes that you are already familiar with the basic structure of the experiment map, and know how to add data processing blocks to it. To learn how to add data processing blocks to the experiment map, click here.
Align
Align is the most basic data processing block. It retrieves the data from the plates in one or more executions, then aligns it with experimental metadata for you to download or use in other data processing blocks.
Tip: You must align your data before you add any other data block to the experiment map.
After you add Align to the experiment map, you can connect it to any execution. If the execution contains some data files, Align will only display information about the plates that contain those data files. If none of the plates contain any data files, Synthace will display an error message.
Use the Variables panel to choose which columns Synthace includes in the Data table. To learn more, click here.
Append Data
Append Data joins datasets together. Use it whenever more than one instance of Align contains data that you want to combine for use downstream or to download.
View Data
Use View Data to analyze your data in three tabs as either: configurable scatter plots (on X-Y View), plate-based heatmaps (on Plate View) or a data table (on Data Summary). View Data always opens on X-Y View with an initial single scatter plot displayed.
You can only create View Data using a single instance of Align or Append as its input. It will have access to all the columns of the aligned data, regardless of whether you only selected a subset of the data in Align when you last used it.
Tip: There is a Save button in the top right of View Data. Click it to ensure that View Data loads in the same state the next time you use it, otherwise it will revert to the default state.
X-Y View
Use X-Y View to create simple scatter plots of pairs of columns. By default, it only displays one plot. To add more plots, click Add Plot. Click the Remove button under a plot to delete it.
Customize a plot
Click Settings to select the desired Horizontal (X) and Vertical (Y) axes from the dataset. You can use a third column from the dataset to control the color of the points.
If you use numerical data to control the point colors, Synthace displays a slider underneath the plot. Use it to filter the plot using the data values. Unselected points will be smaller and appear ghosted out. Additionally, you can use the Jitter tick box to control the spread of the data points.
Controls
Click a control to highlight it. If a control is highlighted, you can perform its action. To learn more, click here.
Plate View
Plate View displays a heatmap for each plate in the dataset. Each one depicts the value for a particular column of data as the color of each well (using up to 9 shades of blue), and uses gray for missing values.
Click Add plate layout to create a plot.
Click the drop-down beneath Add plate layout to select the dataset column that you want to visualize, as well as its colors.
Click Settings to choose the number of color gradations.
Click Remove to delete the plot.
The two icons in the top-right are Save and Hover.
Click Save to download a series of PNG files, one for each plate.
Click Hover to determine whether or not hovering over a well displays the specific value of the plotted data value.
Data Summary
Use the Variables panel to choose which columns Synthace includes in the Data table. To learn more, click here.