The main idea of the germination app is to determine when a plant or group of plants reached a certain threshold. This threshold can be any of the
growth parameter (e.g. a certain minimum height to detect germination or also a certain average color to quantify flowering date).
After you made your selection of the experiment and applied the desired filtering, aggregation and grouping in the overview you can either use the Boxplot view in the germination app to get an overview for all sample groups (unique combination of genotype and treatment) or you can use the Map view to get feedback when individual units have reached the desired threshold.
Before going into detail on the two views inside the germination app let’s quickly open the settings bar and have a look at what settings can be made to change the analysis. To do that, open the Map View of the Germination App and then open the settings bar on the right hand side of the screen.
There are two settings that you can change inside this analysis app. The first is the value of the threshold. The idea of this threshold is that a plant is germinated when it has a measurement value above the threshold. The threshold is always in the unit of the parameter that you have currently selected. You can see and also change that parameter in the center of the canvas below the progress bar. If you are not sure about the values that you see just click on the histogram button.
The histogram you now see is a distribution of the selected value across the entire dataset you have selected for analysis. The red line shows the threshold that you have set.
The second setting that you can change is the Threshold Occurance. The idea of this setting is that you can choose if you want to pick the date on which a unit has first reached the threshold or the last time it crossed the threshold.
To understand this better simply select last and click on one of the units in the center of the canvas (ideally one that does show a germination date). You should see a growth curve like displayed below with the selected parameter on the Y axis and the days after start of analysis (DAS) on the X axis. The dashed red line represents the threshold that you set and the green line shows the recoreded data for this specific unit. You can see in the example below that the first time the threshold was reached was around 6 DAS. However, after this the plant shortly goes below the threshold again. Finally, at 7.7 DAS it goes above the threshold and stays above it. Hence, if we choose first as the Threshold Occurance it will give 6 DAS as a result as this was the first time the unit was above threshold. If we set Threshold Occurance to last it will give 7.7DAS as indicated in the example below because it was the last time when the data crossed the threshold line.
These settings are the same for both views. Let’s therefore explain the views in detail now.
The boxplot view visualizes the spread of germination within one sample group. It can be used to see how homogenous the threshold is reached within one sample group or what the difference of germination date is between sample groups. The wider the spread of the boxplot the more variance there was within the germination. Plants that did not reach the threshold will not be considered on the plot.
The example below shows a set of 8 genotypes and 2 treatments (16 sample groups). On the X axis you see the absolute germination date. For each sample group a boxplot is shown. The centre line in the boxplot shows the date when 50% of the sample group germinated. The lower and upper ends of the box represents the 25% and 75% quantiles. The whiskers represent the 1.5x interquantile distance form the median.
The map view shows on a color scale when individual units reached the threshold for each block of the experiment. Especially for trays with many samples this view can be nice to visualize what units reached the threshold when. The result is shown in days after start of analysis (DAS). If the value is Infinite (inf) the unit never reached the threshold. If there are multiple blocks ins your experiment you can change the current displayed block in the settings bar on the right hand side in the visualization options.