Problem having interpretation GSEA bar diagram

Question

[bookorg]

Hi I have analyzed my common DEG and generated plot to see the involvements of my DEG in several pathaway but I am facing some trouble to interpret the plot .I did dot plot visualization.

[rpolicastro]

Can you post the plot or an example?

[bookorg]

This is the plot.I am not sure what the activated and suppressed means.In fact I also confused about count .What does counts means.And finally the X axis which denotes gene ratio.how the gene ratio calculated..How the 0.5,0.6,0.7,0.8 comes by calculation.I am totally confused about that.And in that figure there are different ratio dot.What does different ratio dot means.

[Basti]

Activated and suppressed refer to the normalized enrichment score (NES). A positive NES indicates that genes in your pathway are mostly upregulated so the pathway is "activated" -> it is very well explained here : question about GSEA

Count is the number of genes you provided that contributes to the pathway

GeneRatio is simply explained here : ClusterProfiler : What is GeneRatio and BgRatio?

[bookorg]

Thank you for your reply.But I need to clear it more thing precisely.Suppose I got 100 DEG.So from that 100 DEG,how much DEG got positive NES ,that genes are actively expressed in that particular pathway.??

In counts-there are several types of black circle .What is the relation between the black circle and inside the bar diagrame dot??

Finally I have another question-When i found commone DEG by analysis ,I found there up and down regulated genes based on logFC.So what is the relevance between this logFC and NES.Because in both term upregulated term is used