cnetplot and barplot don't show top ranked GO enrichments.
1
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Entering edit mode
5 weeks ago
Shakiba ▴ 20

Hi,

I plotted the cnet plot with enrichResult objects. Object 1 was my filtered data with absolute log2 fold change more than 1, and object 2 was my filtered data with absolute log2 fold change more than 1.5. My enriched results are more in object 1, which is expected because I have more genes. But they show me fewer results when I want to plot barplot and cnetplot. I don't know why.

Here is my code.

p_cnetplot <- cnetplot(ego, categorySize="count", showCategory = 10, foldChange=OE_foldchanges, layout = "kk", color_category='tan2', node_label = "all", cex_label_gene = 2, cex_label_category = 1.5, colorEdge = FALSE) p_cnetplot <- p_cnetplot + ggtitle(title_str) + theme(plot.title = element_text(hjust= 0.5, size = 30))
p_barplot <- barplot(ego, showCategory = 30, font.size = 20, label_format = 100, order = FALSE)

absolute log2 fold changes > 1.5

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absolute log2 fold changes > 1

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barplot Goenrichment cnetplot • 220 views
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1
Entering edit mode
5 weeks ago
Shakiba ▴ 20

Hello, I found there is no problen with cnetplot. It just shows the enriched pathways and it is correct. Thank you

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