Hello Biostars! 

I hope you are shining bright!

Today, I'm dealing with a very basic problem that's plotting lines color change. It's very easy in general plot function and ggplot. 
But in case of a function by ChIPseeker  - 'plotAvgProf2', I'm not able to figure how to give arguments as there's not default argument like 'col' or 'colour' in the function :

    plotAvgProf2            package:ChIPseeker             R Documentation
    
    plotAvgProf
    
    Description:
    
         plot the profile of peaks that align to flank sequences of TSS
    
    Usage:
    
         plotAvgProf2(peak, weightCol = NULL, TxDb = NULL, upstream = 1000,
           downstream = 1000, xlab = "Genomic Region (5'->3')",
           ylab = "Read Count Frequency", conf, facet = "none", free_y = TRUE,
           verbose = TRUE, ...)
         
    Arguments:
    
        peak: peak file or GRanges object
    
    weightCol: column name of weight
    
        TxDb: TxDb object
    
    upstream: upstream position
    
    downstream: downstream position
    
        xlab: xlab
    
        ylab: ylab
    
        conf: confidence interval
    
       facet: one of 'none', 'row' and 'column'
    
      free_y: if TRUE, y will be scaled by AvgProf
    
     verbose: print message or not
    
         ...: additional parameter

I don't even how to edit the function too :

    > plotAvgProf2
    function (peak, weightCol = NULL, TxDb = NULL, upstream = 1000, 
        downstream = 1000, xlab = "Genomic Region (5'->3')", ylab = "Read Count Frequency", 
        conf, facet = "none", free_y = TRUE, verbose = TRUE, ...) 
    {
        if (verbose) {
            cat(">> preparing promoter regions...\t", format(Sys.time(), 
                "%Y-%m-%d %X"), "\n")
        }
        promoter <- getPromoters(TxDb = TxDb, upstream = upstream, 
            downstream = downstream)
        if (verbose) {
            cat(">> preparing tag matrix...\t\t", format(Sys.time(), 
                "%Y-%m-%d %X"), "\n")
        }
        if (is(peak, "list")) {
            tagMatrix <- lapply(peak, getTagMatrix, weightCol = weightCol, 
                windows = promoter)
        }
        else {
            tagMatrix <- getTagMatrix(peak, weightCol, promoter)
        }
        if (verbose) {
            cat(">> plotting figure...\t\t\t", format(Sys.time(), 
                "%Y-%m-%d %X"), "\n")
        }
        if (!(missingArg(conf) || is.na(conf))) {
            p <- plotAvgProf.internal(tagMatrix, xlim = c(-upstream, 
                downstream), xlab = xlab, ylab = ylab, conf = conf, 
                facet = facet, free_y = free_y)
        }
        else {
            p <- plotAvgProf.internal(tagMatrix, xlim = c(-upstream, 
                downstream), xlab = xlab, ylab = ylab, facet = facet, 
                free_y = free_y)
        }
        return(p)
    }
    <bytecode: 0x14adad08>
    <environment: namespace:ChIPseeker>

By default, it gives blue n brown colour for 2 samples . I need to change that.
Please help me out. Thank you in advance :)
Please consider this alternative :

https://github.com/GuangchuangYu/ChIPseeker/issues/89

All the best!