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This article mainly introduces the relevant knowledge of "how to draw MA diagram in R language". Xiaobian shows you the operation process through actual cases. The operation method is simple, fast and practical. I hope this article "how to draw MA diagram in R language" can help you solve the problem.

MA plot is M-versus-A plot, also known as Bland-Altman plot before the advent of chip data processing, named after the inventor, while MA plot is named after the plot of M and A, M is the abbreviation of minus, representing the difference between two values, and A is the abbreviation of add, representing the sum of two values. MA plots are also referred to as Ratio-Intensity (RI) plots, and MA is also short for micro-array.

MA Map Introduction

MA map is mainly used in genome data visualization to realize the display of data distribution. It was mainly used in DNA chip data in the early days, but now it is often used to display the results of gene differential expression analysis in high-throughput sequencing data.

M is usually used for Y axis, A is usually used for X axis.

M often corresponds to log2FC of gene expression changes between groups compared to differences obtained by differential expression analysis.

A can be calculated using FPKM of the difference control group. If R and G represent the difference control group, the average FPKM of R group genes and the average FPKM of G group genes can be calculated.

MA drawing

First prepare the data:

The first column is the gene ID, *_FPKM is the FPKM value of the sample (column names must contain "FPKM"), the fourth column is FDR, the fifth column is log2FC, and the sixth column is gene up-down information.

Then, we use R language to draw MA diagram, code is as follows:

### load libraryrequire(ggplot2)library(RColorBrewer)library(getopt)mycol

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