Creates a heatmap of copy number profiles from segment files.
facets.heatmap( seg = NULL, filenames = NULL, path = NULL, patients = NULL, min.purity = 0.3, epsilon = 0.005, ordered = NULL, outcome = NULL, adaptive = FALSE )
Arguments
| seg | a segmentation file containing the segmentation information of multiple patients |
|---|---|
| filenames | the names of the segment files to be loaded and processed (Note must end in ".Rdata"). |
| path | the relative path to the files folder from your current directory |
| patients | the names of the patients of the respective filenames. Default simply 1 to number of files. |
| min.purity | the minimum purity of the sample required to be kept in the final dataset. Default is 0.3. |
| epsilon | level of unions when aggregating segments between |
| ordered | order in which patients should be printed. Default NUll leads to hierarchical clustering. |
| outcome | for seg file only, if outcome associated with study it will be printed along the x axis for each patient |
| adaptive | CNregions option to create adaptive segments |
Value
p a heatmap corresponding to the segment files inputted
Examples
library(gnomeR) library(dplyr) library(dtplyr) patients <- as.character(unique(mut$Tumor_Sample_Barcode))[1:1000] patients.seg <- as.character(unlist(clin.sample %>% filter(Sample.Identifier %in% patients, as.numeric(as.character(Tumor.Purity)) > 30) %>% select(Sample.Identifier))) facet <- facets.heatmap(seg = seg, patients=patients.seg[0:100])#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#> Warning: Problem with `mutate()` input `chrom`. #> ℹ NAs introduced by coercion #> ℹ Input `chrom` is `as.numeric(as.character(.data$chrom))`.#> Warning: NAs introduced by coercion#>facet$p
