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

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