Circos plot with logfold change RNA seq data
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8 weeks ago
aranyak111 • 0

Circos plot with logfold change data.I am new to circos plot analysis and have been trying to use the cyclize package. I want to display mRNA differential gene expression data based on data analyses of 8 libraries and links between their respective target genes. The dataset I am working with looks like this

geneid baseMean log2FoldChange lfcSE stat pvalue padj KDR1 KDR2 KDR3 Ago.1 Ago.2 Ago.3 Gene name ENSDARG00000038147 2590.2 1.701675 0.067331 25.27333 6.28E-141 3.64E-137 3767.297 4087.186 4087.186 1265.112 1175.587 1158.831 hbbe3 ENSDARG00000067964 352.7761 2.195124 0.119682 18.34131 3.87E-75 6.74E-72 616.2616 573.3527 573.3527 102.8945 119.6455 131.1497 slc6a5.

I have thousands of genes and there are 8 libraries like this that will be adjusted based on adjusted p-values. The R scripts I am using to do a somewhat closer plot is like this

library(circlize)
circos.par("track.height" = 0.1)
circos.initialize(df$sectors, x = df$x)
circos.track(df$sectors, y = df$y,
    panel.fun = function(x, y) {
        circos.text(CELL_META$xcenter, 
            CELL_META$cell.ylim[2] + mm_y(5), 
            CELL_META$sector.index)
        circos.axis(labels.cex = 0.6)
})
col = rep(c("#FF0000", "#00FF00"), 4)
circos.trackPoints(df$sectors, df$x, df$y, col = col, pch = 16, cex = 0.5)
circos.text(-1, 0.5, "text", sector.index = "a", track.index = 1)
bgcol = rep(c("#EFEFEF", "#CCCCCC"), 4)
circos.trackHist(df$sectors, df$x, bin.size = 0.2, bg.col = bgcol, col = NA) 

after loading the dataframe. Yet I am far away to generate a plot like what is needed. I want to have a plot like this. Any help will be useful.

Bioinformatics • 322 views
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not sure, but it seems this circos plot is generated by http://circos.ca/

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I have tried every documentation of Circos after installing it in the server without much success.

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