Question: Plotting confidence intervals with NA values

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viniciushs.z •

**20**wrote: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 statment 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!