multi-group GO, Pathway enrichment bubble plot
Introduction
Bubble plot is generally used in GO, KEGG pathway enrichment analysis, in which p values are represented by colors, gene counts are represented by bubble size.
Please use
GO, Pathway Enrichment Analysis or
metascape to get the enrichment results, and then plot.
Input data instructions
Input data contain 5 columns: the first column is categories, such as BP, CC, MF;
the second column is GO or KEGG Pathway term (display in Y axis);
the third column is enrichment (display in X, if no, replace by others, such as gene ratio, -log10(p), count;
the fourth column is p (or FDR, data range 0-1), represents colors;
the fifth colunn is gene count (size of bubble).
Examples from papers
Gene expression profiling and functional analysis reveals that p53 pathway-related gene expression is highly activated in cancer cells treated by cold atmospheric plasma-activated medium Fig 4
1) How to plot?
1, Prepare data
2, Open with excel, and change into the same format as the example
3, Copy and paste data into the input frame
4, Select parameters
5, Submit and download figure files
2) Why NO figure generated?
Script need strigent input format, please read the instructions and examples carefully.
3) How to cite?
2000+ papers in (Google Scholar)
Tang D, Chen M, Huang X, Zhang G, Zeng L, Zhang G, Wu S, Wang Y. SRplot: A free online platform for data visualization and graphing. PLoS One. 2023 Nov 9;18(11):e0294236. doi: 10.1371/journal.pone.0294236. PMID: 37943830.
4) FAQs