I would like to plot confidence intervals to a data with NAs, using Gviz package. I modified manual example to expose my problem. First as the manual expose:

    library(Gviz)

    ## Loading GRanges object
    data(twoGroups)

    ## Plot data without NAs
    dTrack <- DataTrack(twoGroups, name = "uniform")
    tiff("Gviz_original.tiff", units="in", width=11, height=8.5, res=200, compress="lzw")
    plotTracks(dTrack, groups = rep(c("control", "treated"),
                                    each = 3), type = c("a", "p", "confint"))
    graphics.off()

#Now, using data with `NA` values and `na.rm=TRUE` statment:

      ## Transforming in data frame
      df <- as.data.frame(twoGroups)

    ## Input NAs to look like my real data
    df[ df <= 0 ] = NA
    df <- df[,-4]
    df <- df[,-4]
    names(df) <- c("chr", "start", "end", "control", "control.1", "control.2", "treated", "treated.1", "treated.2")

    ## Plot with NA
    df <- makeGRangesFromDataFrame(df, TRUE)
    dftrack <- DataTrack(df, name = "uniform")
    tiff("Gviz_NA.tiff", units="in", width=11, height=8.5, res=200, compress="lzw")
    plotTracks(dftrack, groups = rep(c("control", "treated"),
                                     each = 3), type = c("a", "p", "confint"), na.rm=TRUE)
    graphics.off()

Please note that I included the na.rm=TRUE statement in plotTracks function, which allowed the computation of the line following the mean. However, the shaded area which represents the confidence interval, can't be estimated where I have NA values, even with the na.rm=TRUE.

Any ideas to deal with this issue? Thank you!