CellPhoneDB results

Question

[torabian.p]

I used CellPhoneDB package in Linux and I got some results. But, the statistical legend is not clear to me. Is anybody can clarify them? For more information, this package takes deconvolution data as input and gives ligand-receptor interactions. The molecules on the left side are ligands-receptors. However, I am not sure about the size of the circles and the color range.

Answer 1

[Istvan Albert]

The legend means that:

1. The color of the circle represents the effect size expressed as log 2,
2. The diameter of the circle corresponds to the pvalue as log 10,

For example, a -4 and 3 for each would mean you have an effect size of 1/16 (2^-4) and the p-value is 1/1000 (10^-3)

For what is worth the visualization is quite questionable, to say the least - at a glance it is hard to understand what it shows.

[torabian.p]

Thank you so much Istvan. Yes, it is pretty complex once you have to explain it to others what you got from it simply.

[torabian.p]

Just one more thing. By effect size, do you mean the interaction? For example, the more interaction, the more effect size?

[Istvan Albert]

the effect size is the "change" that is claimed to be present. Could be a difference, but it could also be expressed as a fraction, I have not read the paper so I am not sure what is in this case. Something that is computed between the two molecules.

Now the effect size is connected to the p-value,

The p-value indicates the likelihood of observing an effect of that size (or bigger) by chance alone

[torabian.p]

Thank you @Istvan This package talks about ligand-receptor interactions and the dot plot is the results I got. It seems the warmer colors represent more interactions between molecules.