User: Peter.Wood

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Peter.Wood0
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Posts by Peter.Wood

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Plotting the X chromosome using the zoom function
... Using the zoom function in OmicCircos, I am trying to plot the gene expression for the  X chromosome. #insert chromosome X zoom <- c(X, X, 939245.5, 154143883, 343.7, 376.7); # insert circos circos(R=350, cir="hg19", W=4, type="chr", print.chr.lab=T, scale=T, zoom=zoom); circos(R=120, cir="h ...
omiccircos gene expression gene set enrichment written 4.3 years ago by Peter.Wood0 • updated 4.2 years ago by yhu50
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Unknown coordinates in highlight and zoom functions.
... I am trying to highlight and zoom specific segments of a OmicCircos plot. In the highlight function their are a number of coordinates which correspond to the region of the circos that will be highlighted. For example, the highlight function for figure 1 in OmicCircos: A Simple-to-use R Package for ...
zoom omiccircos highlight written 4.3 years ago by Peter.Wood0 • updated 4.2 years ago by Biostar ♦♦ 20
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OmicCircos text fonts
... Just wondering whether it is possible to change fonts for a OmicCircos plot in R? Thanks ...
omiccircos written 4.3 years ago by Peter.Wood0 • updated 2.5 years ago by maguirre10
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Larger values masking others for OmicCircos heatmap
... I am wondering whether the heatmap scale for the circos plot can be specified to each gene. At the moment the  highly expressed genes are masking the others so that differential expression patterns are not being shown for all of the genes.  circos(R=110, cir=db, W=200, mapping=gene.expression,  c ...
omiccircos circos differential gene expression written 4.4 years ago by Peter.Wood0 • updated 4.4 years ago by Irsan6.8k
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Comment: C: Circos plot heatmap
... The line circos(R=110, cir=db, W=200, mapping=gene.expression, col.v=4, type="heatmap2", col.bar=T, lwd=1); generates a heatmap, but its scale is universal for every gene plotted with the extreme values of some genes masking the other gene expression patterns. ...
written 4.4 years ago by Peter.Wood0
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Circos plot heatmap
... In the Circos plot, the heatmap is distorted by extreme values by certain genes. I am inquiring whether the heatmap can be applied independently to each gene that  will allow me to view the gene expression between each experiment groups for every gene. par(mar=c(2, 2, 2, 2)); plot(c(1,800), c( ...
differential gene expression heatmap written 4.4 years ago by Peter.Wood0 • updated 11 months ago by Biostar ♦♦ 20
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How to create an anchor for OmicCircos
... Could someone please explain how to create an anchor in the OmicCircos package from a data frame. My previous attempts have failed with the OmicCircos package uploading the hg18/hg19 genome rather than my gene set. Thanks. ...
gene set enrichment analysis gene expression written 4.4 years ago by Peter.Wood0 • updated 4.2 years ago by yhu50
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Making a circos plot to show expression for a gene set rather than whole genome
... Hello, I am a new user to the OmicCircos package and the R code. For a little while I have been trying to create a circos plot to show the expression of a gene set. However, after constructing data frames with gene names and segment sizes, the segAnglePo and sim.circos functions consistently revert ...
omiccircos gene set written 4.4 years ago by Peter.Wood0 • updated 4.2 years ago by Biostar ♦♦ 20

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