Description Usage Arguments Value Examples
This function adds chunk information for wrapping an alignment and annotations across multiple rows. This will also split individual annotations across rows.
1 | chunkAnnotation(anno_df, chunks)
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anno_df |
an annotation data frame from readAnnotationFile with attached alignment positions from addAlnPosToAnno |
chunks |
a data frame of chunks to facet an alignment/annotation data frame across |
anno_df with the addition of chunks columns (and potentially extra rows) for facetting
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## first make a gene info DF
geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))
## read in an annotation DF
anno_df <- readAnnotationFile(filename = system.file("extdata",
"AFB_annotations.csv", package = "r1001genomes"), gene_info = geneInfo )
## make an alignment DF
IDs <- c("AT3G62980.1", "AT3G26810.1")
alignment <- alignCDS(IDs)
aln_df <- makeAlnDF(alignment[[2]])
aln_df <- chunkAlnDF(aln_df)
chunks <- makeChunksDF(aln_df)
anno_df <- addAlnPosToAnno(anno_df, aln_df)
chunkAnnotation(anno_df, chunks)
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