GO, Pathway enrichment bubble plot
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
to get the enrichment results, and then plot.
Input data instructions
Input data contain 4 columns: the first column is GO or KEGG Pathway term (display in Y axis);
the second column is enrichment (display in X, if no, replace by others, such as gene ratio, -log10(p), count;
the third column is p (or FDR), represents colors;
the fourth colunn is gene count (size of bubble).
Optional for fifth columns, plot by class with facet, for example BP, CC, MF.
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
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?
162 papers cited us (Google Scholoar). You can cite the original package, or using the following format:
Heatmap was plotted by http://www.bioinformatics.com.cn, a free online platform for data analysis and visualization.