Tuesday, March 19, 2013

Manhattan plot using Excel

Manhattan plots

Manhattan plots are simply scatter plots where the physical distance are in x axis and p-value or -log10(pvalue) in Y axis. As there are multiple linkage groups, we might want to create a gap and use different color or symbol for different chromosomes.

(1) Data manipulation: We need to create additional column where we put cumulative distances (column dposition) starting from first chromosome, so that we can plot all chromosome in a single scatter plot. If would like to create gap between chromosomes simply add some (may be 10% of average chromosomal length ) value to first value.

(2) Plot dposition (X) vs Y  is -log10(pvalue) using scatter plot function. In addition if would like to use different color or symbol type for different chromosomes manually select each chromosome X and Y cell values. It is much easier to select if the data is in wide format than long format. Now you can remove the all -log10(Pavlue) series. Also you can remove the cumulative positions.

The plotting is similar in other excel version. The idea is basically same. The example output look like the following in 2013, with p-values populated and using different styles for scatter plot.

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