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sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
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Cell chat pathway bar plot of single pathway is not consistent with heatmap color (communication probability values) #361

Open kulansam opened 2 years ago

kulansam commented 2 years ago

Hi,

Thanks to everyone who involved in the development of cell chat software. I have used cell chat for cell-cell communication analysis on my dataset. I am trying to visualize the individual signaling pathway using the heatmap, but in the map, the color of communication probability values is not consistent/match with the top and right bar plot (Is it a sum of communication probability scores right?)

Please see the below figure, the disease condition has a much darker color (which means a high communication score) than the wild-type condition. however, why the communication score is lower for disease-condition. Is it due to any normalization in cell chat? please help me out? Picture1

sqjin commented 2 years ago

@ksbioinfo We did not control the color scale in different plots. Thus, comparison of the colors across different plots does not make sense here.

kulansam commented 2 years ago

@sqjin Thanks for your comment. If so, then why this figure shows the color scale? Could you please explain to me a little clear?

Also, Why the bar plot values are not matching with the color map. For example, in the above figure (disease), the first bar has a cumulative frequency of around 0.3 but it has darker red colors (than wild-type) in the respective coloum. According to the color scale, the cumulative frequency is not matching. why it is like this?

In addition to that, which function should I use to get these values that are used in this heatmap?