This belongs to the first diagnostic plots (raw mismatches) generated by GRAND3.
PlotMismatchPositionForType(
data,
genomic,
read,
orientation = NULL,
category = NULL,
max.pos = 2500
)a list with a ggplot object, a description, and the desired size for the plot
a grandR object
the nucleotide as it occurs in the genome
the nucleotide as it occurs in the read
restrict to either Sense or Antisense; can be NULL
restrict to a specific category (see GetDiagnosticParameters); can be NULL
remove everything behind this position
For all positions along the reads (x axis; potentially paired end, shown left and right), show the percentage of a specific mismatch type for all samples. Positions outside of shaded areas are clipped. Uncorrected and Retained means before and after correcting multiply sequenced bases. Sense/Antisense means reads (first read for paired end) that are (based on the annotation) oriented in sense or antisense direction to a gene (i.e. this is only relevant for sequencing protocols that do not preserve strand information).