Question: Plotting confidence intervals with NA values

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Vinicius Henrique da Silva •

**40**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 library(GenomicRanges) 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!

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modified 4.2 years ago
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James W. MacDonald ♦

**52k**• written 4.2 years ago by Vinicius Henrique da Silva •**40**