Question: Plotting and Visualizing large number of genes into chromsome
gravatar for rice.researcher
5.2 years ago by
Korea, Republic Of
rice.researcher150 wrote:


I have a list of arounfd 5000 rice genes. I would like to display those genes in rice chromosome. I tried with Rcircos, tool is good but it can map upto a few genes. So I am in trouble.!! I know about circos but it is beyond my limit to execute. Do anyone of you have an idea about method/any software suit which can be used to visualize large number of genes to chromosome?

It is ok for me if I can represent genes as even dots (rather than with gene label). My aim is to make a distribution plot chromosome .



ADD COMMENTlink modified 3.3 years ago by bernatgel2.5k • written 5.2 years ago by rice.researcher150

Do you really want to show all 5000 at once? Realistically, that's going to be such a busy plot that it'll be quite difficult to get anything out of it. Presumably you're looking to show some kind of connection between genes, so likely using just a subset of genes will suffice.

ADD REPLYlink written 5.2 years ago by Devon Ryan95k

I thought there might be some tools which provide a scattered plot kind of mapping ( I mean many dots) onto chromosome. My  list is having 3450 genes. In this case, I am not using connector to link genes@Devon Ryan 

ADD REPLYlink written 5.2 years ago by rice.researcher150

I would plot the density of genes along the chromosome as a line. dots is still not simple enough

ADD REPLYlink written 5.0 years ago by Ido Tamir5.0k

"I know about circos but it is beyond my limit to execute" tell us what's the problem or ask the circos mailing list.

ADD REPLYlink written 5.2 years ago by Pierre Lindenbaum128k
What do you mean by plotting a gene? Do you want to plot the gene body (exon-intro structure), or do you have a value for each gene and you want to plot them as points, or anything else?
ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by Irsan7.1k
gravatar for bernatgel
3.3 years ago by
Barcelona, Spain
bernatgel2.5k wrote:

In R you can use the Bioconductor package karyoploteR to create the ideogram and plot the genes. You can plot all genes individually (either as regions or as points...) or compute the gene density over the genome using a non-overlapping sliding window, using kpPlotDensity. To create this plot you'll need to have the BSgenome.Osativa.MSU.MSU7 package installed, wich would not be necessary for human, mouse and some other organisms.

As an example we can create 5000 random "genes" and plot them. Above the ideograms we'll plot the gene density and below them the actual genes using a semitransparent color to show the accumulation of genes in certain regions.


#Create 5000 regions as mock genes
genes <- createRandomRegions(5000, length.mean=3000, genome="MSU7")

kp <- plotKaryotype(genome="MSU7", plot.type=2, cex=1.6)
kp <- kpPlotDensity(kp, data=genes, col="dodgerblue")
kpAxis(kp, ymin=0, ymax=kp$latest.plot$computed.values$max.density)
kpPlotRegions(kp, data=genes, data.panel=2, col="#00000044")

enter image description here

You can then customize the appearance of this plot, change its colors, etc... and combine it with any other karyoploteR function. You can find all the information needed in the karyoploteR tutorial

ADD COMMENTlink modified 7 months ago • written 3.3 years ago by bernatgel2.5k
gravatar for Selenocysteine
5.0 years ago by
Dublin, Ireland
Selenocysteine600 wrote:

Hi, perhaps you can use a Manhattan plot? :) I don't really know what you can use for the Y axis, but...

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Selenocysteine600
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