Search
Question: Pathview: visualization of data
0
gravatar for svmichaela
5 weeks ago by
svmichaela0
svmichaela0 wrote:

Dear Weijun,

I am absolutly new in R programing so be gently please. I am using your very nice package Pathview to visualize my expression data, and I am fine-tuning the graphical output towards my needs. I therefore have 2 questions, and would appreciate if you could comment on these:

1. How do I change the scale at the image. I used this command:

pv.out <- pathview(gene.data = as.matrix(dd2[,7:22]), pathway.id = "04640", species = "hsa", gene.idtype = "SYMBOL", limit = list(gene = 100, cpd = 1))

and the scale is from -100 until 100. I have data from RNAseq and I put there levels of gene expression so I have just number from 0 until 100...?

2. pv.out <- pathview(gene.data = as.matrix(dd2[,7:22]), pathway.id = "04640", species = "hsa", gene.idtype = "SYMBOL", limit = list(gene = 100, cpd = 1))

Like this I predicted the metabolic pathway I put there the number of the pathway (example 04640 in this case). What should I do if I don't know which pathway I want?

I'm sorry I'm absolutely beginner. 

Thank you very much.

Michaela

ADD COMMENTlink modified 5 weeks ago by Luo Weijun1.4k • written 5 weeks ago by svmichaela0
0
gravatar for Luo Weijun
5 weeks ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:

Michaela,

Thanks for your interest in Pathview.

Question 1: you can set limit=list(gene=c(0,100), cpd=1) with your pathview() call.

Question 2: you need to do pathway analysis to select significantly perturbed pathway first, you may tools like gage: http://bioconductor.org/packages/release/bioc/html/gage.html. You may check the main vignette and the RNA-seq pathway analysis workflow.

Since you are new in R, you may check our pathview web server:

http://pathview.uncc.edu/

the server not includes pathview function but also a full pathway analysis workflow for multiple types of omics data and their integrated analysis. you can start with the examples.

HTHs.

Weijun

ADD COMMENTlink written 5 weeks ago by Luo Weijun1.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 125 users visited in the last hour