#' Plot ppm error distribution using MaxQuant output
#'
#' @description Uses the output from MaxQuant (evidence.txt) to plot ppm error distribution for the identified peptides.
#'
#' @returns Returns a density plot.
#'
#' @param x The filtered 'evidence.txt' file. Use MQ_remove_CR first to remove contaminants and reverse hits.
#'
#' @example
#' MQ_evidence_ppm_error(filtered_evidence_output)
#'
#' @export
MQ_evidence_ppm_error <- function(x) {
names(x) <- tolower(names(x))
er.ppm <- ggplot(data = x, aes(x = mass.error..ppm., color = experiment))
er.ppm <- er.ppm + geom_density()
er.ppm <- er.ppm + theme_bw()
er.ppm <- er.ppm + xlab("Mass ppm error")
er.ppm <- er.ppm + ylab("Frequency")
er.ppm <- er.ppm + ggtitle("ppm error per sample")
er.ppm <- er.ppm + theme(legend.position = "bottom")
er.ppm <- er.ppm + theme(legend.key.size = unit(0.2, "cm"))
er.ppm <- er.ppm + theme(legend.text = element_text(size = 8))
print(er.ppm)
}
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