Get MS2 match plots from a metIdentifyClass object.
ms2plot( object, database, which.peak = "all", ppm.tol = 30, mz.ppm.thr = 400, path = ".", width = 20, height = 8, interaction.plot = FALSE, range.mz, range.int = c(-1, 1), xlab = "Mass to charge ratio (m/z)", ylab = "Relative intensity", col.lib = "red", col.exp = "black", title.size = 15, lab.size = 12, axis.text.size = 12, legend.title.size = 12, legend.text.size = 10, figure.type = c("png", "pdf"), threads = 3, one.folder = TRUE, show.plot = TRUE )
Arguments
| object | A metIdentifyClass object. |
|---|---|
| database | Used database (databaseClass). |
| which.peak | Peak name(s) or "all". You can use which_has_identification functions to get what peaks have identifications. |
| ppm.tol | MS2 fragment match ppm. |
| mz.ppm.thr | The threshold for m/z error calculation. |
| path | Work directory. |
| width | The width of MS2 spectra match figure (inch). |
| height | The height of MS2 spectra match figure (inch). |
| interaction.plot | Output interactive plot or not. |
| range.mz | m/z range for MS2 spectra match plot. |
| range.int | Relative intensity range. |
| xlab | Title of x axis. |
| ylab | Title of y axis. |
| col.lib | Colour of database MS2 spectrum. |
| col.exp | Colour of experimental MS2 spectrum. |
| title.size | Font size of title. |
| lab.size | Font size of title of axis. |
| axis.text.size | Font size of axis text. |
| legend.title.size | Legend title size. |
| legend.text.size | Legend text size. |
| figure.type | "pdf" or "png". |
| threads | The number of threads |
| one.folder | Output all figure in one folder or not. |
| show.plot | Show plot or just save them. |
Value
A or all ms2 match plot(s).
See also
The example and demo data of this function can be found https://jaspershen.github.io/metID/articles/metID.html
Examples
data("annotate_result", package = "metID") data("msDatabase_hilic0.0.2", package = "metID") peak_name <- which_has_identification(annotate_result) ms2plot(annotate_result, database = msDatabase_rplc0.0.2, which.peak = peak_name[1,1])#> Warning: Removed 26 rows containing missing values (geom_segment).#> Warning: Removed 8 rows containing missing values (geom_segment).
