Question: KOG/COG annotation results chart
gravatar for seta
4.0 years ago by
seta1.2k wrote:

Hi all,

Please accept my apology for this basic question. Regarding KOG/COG annotation presentation, almost everyone use the column chart with colorful columns (for example, please see Figure 3 of enter link description here . I was wondering if there is any specific reason for such a presentation? Which tool was used for drawing this chart with the colorful columns?

Thank you

ADD COMMENTlink modified 3.5 years ago by Farbod3.3k • written 4.0 years ago by seta1.2k
gravatar for Farbod
3.5 years ago by
Farbod3.3k wrote:

Dear Seta , Hi.

Usually It is has been created using ggplot2 in R. I have a complete script for it in here which you cane use in Rstudio.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Farbod3.3k

Hi Farbod. Thank you very much for sharing the script

ADD REPLYlink written 3.5 years ago by seta1.2k

I found this script super helpful, thank you! I do have a few questions though. 1. Is there a way to get rid of the awkward space between the first y major axis tick (0) and the x axis? 2. Do you know how you would add a second legend, like the bottom legend in this pic?


ADD REPLYlink modified 13 months ago • written 13 months ago by mss30
gravatar for dago
4.0 years ago by
dago2.6k wrote:

Well, it is a way to summarize your data (proteins annotated in a genome, transcripts, proteins in proteome and so on). Let's say that you compare two different conditions and you want to get a first glimpse about the variation that this conditions have on the transcripts, you will get a snapshot looking a such graphs. For example in condition 1 more genes involved in Carbohydrate transport and metabolism are transcribed then in condition 2. You can simply do that using Excels, R, SigmaPlot, whatever. You need to have the number of genes/proteins/transcripts for each category and plot them as absolute values or as frequencies.

ADD COMMENTlink written 4.0 years ago by dago2.6k
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