Read before use
1, check data with precheck (windows version) tools
2, data from excel, copy and paste data into the input frame
3, data from txt, must tab-seperated, copy and paste data into the input frame
4, specieal and non-English characters such as #, <, >, %, (, ), α are not friendly
5, use point as decimal separator, not comma. e.g. 3.14, not 3,14 as pi

Required
small data (copy and paste)

large data (upload tab-seperated txt file)


Optional
Figure size
figure width:
figure height:

significant threshold: (horizontal line, input format: 0.00001 or 1e-4):

significant line color:
significant point color:

Density


bin
binsize:
binmin:
binmax:

Colors
lower color:
middle color:
higher color:

Fontfamily


Manhattan plot

Introduction
Manhattan plot is a type of scatter plot, generally used to display many data points with non-zero amplitudes and bigger amplitudes. Often used in GWAS results to display important SNPs. Every point in the figure represents a SNP, Y axis is -log10(p), X axis is chromosomes. Points without larger -log10(P) (smaller p) have stronger relationship with phenotypes or diseases. Generally, the p threshold is 10^-6 or 10^-8.
Input data instructions
The first column is SNP names; the second column is chromosomes (without chr); the third column is locations; and the fourth column is p values. Plotted by CMplot.
Examples from papers： Genome wide association studies for yield and its component traits under terminal heat stress in Indian mustard (Brassica juncea L.) Fig3
Input Example
Output

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