I can confirm that the data points of the transient simulation are not visible if DC simulation is preceding TRAN (electric only, command line spice using the same .spi file is fine).
Disabling DC simulation or putting DC and TRAN in two separate files allows me to plot both datasets (maybe x/y axis range is not reset properly when switching between DC and TRAN plot?).
If you can plot transient datasets, then it comes down to generate the eye plot dataset in your spice code.
For me the axis scale goes out-of-range as soon I either try loading both tran and dc plot, or drag one of the vectors onto the time axis: the scale printed there can be as low as 1e-9 or as high as 1e+3 if the vector is in the 0..5V range.
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I have looked at this issue. There are definitely bugs in the waveform viewer, which I believe I have fixed.
But there are also issues with your data.
You claim that Electric is using the row number instead of a proper value for v(in). But when I look at the .RAW file, I see that the v(in) and v(sweep) values are exactly the same as the row numbers (divided by 1000). They both run from 0 to 5 over the 5000 data points.
So doing an Eye plot is no different than simply plotting v(out).
But there were also bugs in Electric that prevented zooming, panning, and displaying of all data points. These bugs are fixed in the source code repository, and will be part of the release of version 9.05 which will be happening in the next week