I have a query from the FELLA (and R) package.

Question

[lorenzo.campanelli11]

Hi all, I was analyzing some metabolites from an experiment with the FELLA package. I have a problem with the visualization of ratios.

When I plot the metabolite relationships, the text appears in the same color as the metabolite category, making it very difficult to read which metabolite it is talking about. I tried to find the error in the user manual and also by changing the font of the text from the plot function and I had no success. I attach text and image.

>     library(readxl)
>     Lista_uniq_completa <- read_excel("~/Documents/FIL - Lab ECyN/Proyecto FATZEIMER/Fella/DIABLO_FELLA/Lista_uniq_completa.xlsx", 
>                                       sheet = "Lista__Import", col_names = FALSE)
>     Lista_uniq_completa <- read.table("~/Documents/FIL - Lab ECyN/Proyecto FATZEIMER/Fella/DIABLO_FELLA/Lista_Plasma_uniq.txt",
> quote="\"", comment.char="")
>     
>     compounds.epithelial <- as.list(Lista_uniq_completa)
>     compounds.epithelial <- unlist(Lista_uniq_completa)
>     
>     analysis.epithelial <- defineCompounds(
>       compounds = compounds.epithelial,
>       data = fella.data)
>     
>     getInput(analysis.epithelial)
>     
>     getExcluded(analysis.epithelial)
>     
>     analysis.epithelial
>     
>     analysis.epithelial <- runDiffusion(
>       object = analysis.epithelial,
>       data = fella.data,
>       approx = "normality")
>     
>     analysis.epithelial
>     
>     nlimit <- 50
>     vertex.label.cex <- .5
>     
>     pdf(file = "network_fella")
>     plot(
>       analysis.epithelial,
>       method = "diffusion",
>       data = fella.data,
>       nlimit = nlimit,
>       vertex.label.cex = vertex.label.cex,
>       )
>     dev.off()

Thanks!!

[andres.firrincieli]

It is tricky but it can be done.

First, you need to convert analysis.epithelial into an igraph object:

myGraph <- generateResultsGraph(
    object = analysis.epithelial, 
    method = "diffusion", 
    threshold = 0.1, 
    data = fella.data)

then you have to use plotGraph function (plotGraph.R file) but first it need to be modified. Specifically, change the line 180 from vertex.label.color = vertex.color to vertex.label.color = "black"

[lorenzo.campanelli11]

Thank you very much!!! Ir worked.

In order to thange parameters I have to do it in the function right? (like changing node size por example, or r cutoff).

Thanks again!

[andres.firrincieli]

Unfortunately yes; In order to change other parameters you have to modify the function.