Select appropriate dataset for examples and vignette as well

[federicomarini]

Ideally following Plattner et al 2020?

[federicomarini]

The example 1 and 2 in the vignette are taken indeed from Plattner et al.

Apart from the non-identical color scheme (just veeeery similar), it looks exactly the same, so this is reassuring 😃

[FFinotello]

Test cases:

• Blood validation data as in Finotello et al., Fig. S6 (and Plattner et al., Figure 3). Parameters: default. Data sent via email.
• Tumor from melanoma patients treated with kinase inhibitors data as in Finotello et al., Fig. 5a (and Plattner et al., Figure 6). Parameter: tumor=TRUE. Data sent via email.
• Simulation data as in Finotello et al., Suppl. Fig. S1. Parameters: tumor=TRUE, mRNAscale=FALSE. Data available here.
• Tumor data from CRC patients (RNA-seq and cell densities) as in Finotello et al., Fig. S14. Parameters: tumor=TRUE, totalcells=. Data to be sent via email if possible.
• Blood validation data from microarrays (GSE20300). Finotello et al., Suppl. Fig. S4. Parameters: arrays=TRUE. Data to be sent via email.

[federicomarini]

We have now 4 use cases - the one unchecked here could be added at later time points if needed