metaplot_deletions {amplican} | R Documentation |
This function plots deletions in relation to the amplicons for given
selection
vector that groups values by given config group
.
All reads should
already be converted to their relative position to their respective amplicon
using amplicanMap
.
Top plot is for the forward reads and bottom plot is for reverse reads.
metaplot_deletions(alnmt, config, group, selection, over = "overlaps")
alnmt |
(data.frame) Loaded alignment information from events_filtered_shifted_normalized.csv file. |
config |
(data.frame) Loaded table from config_summary.csv file. |
group |
(string) Name of the column from the config file to use for grouping. Events are subselected based on this column and values from selection. |
selection |
(string or vector of strings) Values from config column specified in group argument. |
over |
(string) Specify which column contains overlaps with
expected cut sites generated by |
(deletions metaplot) ggplot2 object of deletions metaplot
Other specialized plots: metaplot_insertions
,
metaplot_mismatches
,
plot_cuts
, plot_deletions
,
plot_heterogeneity
,
plot_insertions
,
plot_mismatches
,
plot_variants
#example config config <- read.csv(system.file("extdata", "results", "config_summary.csv", package = "amplican")) #example alignments results alignments_file <- system.file("extdata", "results", "alignments", "events_filtered_shifted_normalized.csv", package = "amplican") alignments <- read.csv(alignments_file) metaplot_deletions(alignments[alignments$consensus, ], config, "Group", "Betty")