mms2plot: mms2plot
In lileime/mms2plot: Visualization of multiple MS2s for (un)modified peptides

Description Usage Arguments Value Note Author(s) Examples

Visualization of multiple MS/MSs for (un)modified peptides

mms2plot(id_table_path, par_xml_path, mqpar_filepath, output_path,
    min_intensity_ratio = 0.01, pdf_width = 3.35,
    pdf_height = pdf_width/2.4, xmai = 0.15 * pdf_width/3.35,
    ymai = 0.3 * pdf_width/3.35, ppm = 20, y_ion_col = "red",
    b_ion_col = "blue", peaks_col = "grey", ymax = 1.6,
    info_height = 1.5, peptide_height = 1.3, mod_height = 0.07,
    len_annoSpace = 0.1, lwd = 1 * pdf_width/3.35, cex = 1 *
    pdf_width/3.35, show_letterBY = FALSE)

`id_table_path`	File path name of a table that contains MS2 information of identified (un)modified peptides plus a group labelling. The format of MS2 information is referred to as the output file ms2.txt from the Maxquant search software.
`par_xml_path`	Xml file path of parameters for modifications and labelling. The file is the Maxquant parameter file modifications.xml.
`mqpar_filepath`	File path name that includes a list of parameter files for search engines. The parameter file format is referred to as mqpar.xml in Maxquant.
`output_path`	path of output files.
`min_intensity_ratio`	minimal percentage threshold of MS2 intensity, compared with the highest intensity. (default=0.01).
`pdf_width`	The width of a single PSM figure area in inches. The area includes both plot region and outer margin area. The default is 3.35 for a single column. The width is 7 for double-column.
`pdf_height`	The height of a single PSM figure area in inches. The default is pdf_width/2.4.
`xmai`	margin of the figure in number of inches for x axis. (default=pdf_width*0.15/3.35).
`ymai`	margin of the figure in number of inches for y axis. (default=pdf_width*0.15/3.35).
`ppm`	The threshold of mass error in parts per million(ppm): (exactMass-accurateMass)/exactMass*1E6. (default=20).
`y_ion_col`	y ion color. The default is red.
`b_ion_col`	b ion color. The default is blue.
`peaks_col`	color of all M/Z peaks. The default is grey.
`ymax`	The height of the plot region relative to the default. (default=1.6).
`info_height`	The height of MS2 annotation. (default=1.5)
`peptide_height`	The height of peptide sequence annotation in the plot region, relative to the default. (default=1.3)
`mod_height`	The height of modification annotation relative to the location where peptide sequence is annotation. (default=0.07).
`len_annoSpace`	The length of b/y ion annotation segments.(default=0.1).
`lwd`	line width relative to the default. (default=pdf_width/3.35).
`cex`	A numerical value giving the amount by which plotting text and symbols is magnified relative to the default.(default=pdf_width/3.35).
`show_letterBY`	Logical: should "b" or "y" characters are shown on the peak annotation? The default is FALSE.

No value is returned.

See vignettes for more details

Lei Li

## Not run: 
# Generate mms2plot for TMT labelling
# id_table_path expands the Maxqaunt output msms.txt by adding "label" column
id_table_path = "inst/extdata/TMT/msms_TMT.txt"
par_xml_path = "inst/extdata/modifications.xml" # Maxquant modifications.xml
# mqpar_filepath contains mqpar.xml with full file path and PPM cutoff
mqpar_filepath = "inst/extdata/mqpar_batch.txt"
output_path = "inst/extdata"
mms2plot(id_table_path, par_xml_path, mqpar_filepath, output_path)

# Generate mms2plot for SILAC labelling
id_table_path = "inst/extdata/silac/msms_SILAC.txt"
par_xml_path = "inst/extdata/modifications.xml"
mqpar_filepath = "inst/extdata/mqpar_batch.txt"
output_path = "inst/extdata"
mms2plot(id_table_path,par_xml_path,mqpar_filepath,output_path,pdf_width=7)

# Generate mms2plot for dimethyl labelling
id_table_path = "inst/extdata/Dimethyl_Labelling/msms_dim.txt"
par_xml_path = "inst/extdata/modifications.xml"
mqpar_filepath = "inst/extdata/mqpar_batch.txt"
output_path = "inst/extdata"
mms2plot( id_table_path, par_xml_path, mqpar_filepath, output_path )

## End(Not run)