plot_prot: Protein structure diagram.

In missuse/ragp: Mining for Hydroxyproline rich glycoprotein sequences

Description

Plots a diagram of protein structure based on several types of annotations and predictions.

Usage

plot_prot(
  sequence,
  id,
  hyp_col = "#868686FF",
  gpi_col = "#0073C2FF",
  nsp_col = "#CD534CFF",
  ag_col = "#E5E5E5FF",
  tm_col = "#EFC000FF",
  hyp = TRUE,
  gpi = c("bigpi", "predgpi", "netgpi", "none"),
  nsp = c("signalp", "signalp5", "none"),
  ag = TRUE,
  tm = c("phobius", "tmhmm", "none"),
  domain = c("cdd", "hmm", "none"),
  disorder = FALSE,
  hyp_scan = if (ag == TRUE && hyp == TRUE) TRUE else FALSE,
  dom_sort = c("ievalue", "abc", "cba"),
  progress = FALSE,
  gpi_size = 4,
  gpi_shape = 18,
  ...
)

Arguments

sequence	String representing a protein amino acid sequence.
id	String representing a protein identifier. Will be converted using make.names.
hyp_col	Plotting color of predicted hydroxyproline positions. At default set to: '#868686FF'.
gpi_col	Plotting color of the predicted omega site (glycosylphosphatidylinositol attachment). At default set to: '#0073C2FF'.
nsp_col	Plotting color of the N-terminal signal peptide. At default set to: '#CD534CFF'.
ag_col	Plotting color of the AG glycomodul spans. At default set to: '#E5E5E5FF'.
tm_col	Plotting color of the transmembrane regions. At default set to: '#EFC000FF'.
hyp	Boolean, should hydroxyprolines be plotted.
gpi	A string indicating if get_big_pi (gpi = "bigpi"), get_pred_gpi (gpi = "predgpi") or get_netGPI (gpi = "netgpi") should be called when predicting omega sites. To turn off omega site prediction use gpi = "none". At default set to "netgpi". Alternatively the output data frame of the mentioned functions (called with simplify = TRUE) can be supplied.
nsp	A string indicating if get_signalp5 (nsp = "signalp5") or get_signalp (nsp = "signalp") should be used to obtain N-sp predictions. Alternatively a data frame containing three columns: a character column "id" indicating the protein id as from input, a logical column "is.signalp" and an integer column "sp.length". See get_signalp5 or get_signalp for details.
ag	Boolean, should the AG glycomodul spans be plotted.
tm	A string indicating if get_phobius (tm = "phobius") or get_tmhmm (tm = "tmhmm") should be used to obtain transmembrane region predictions. Alternatively a data frame with two columns: a character column "id" indicating the protein id as from input and a "prediction" column containing the topology of the transmembrane regions (example "42o81-101i108-126o"). To turn off tm prediction use tm = "none".
domain	A string indicating if get_cdd (domain = "cdd") or get_hmm (domain = "hmm") should be used to obtain domain annotation. Alternatively a data frame with five columns: a character column "id" indicating the protein id as from input, a character column "acc" indicating the accession of the domain hit, a character column "desc" indicating the description of the domain hit, a numeric column "align_start" indicating the start of the domain hit, a numeric column "align_end" indicating the end the domain hit.
disorder	Boolean, should disordered region predictions obtained using get_espritz be plotted. Alternatively the output data frame from get_espritz (called with simplify = TRUE) can be supplied.
hyp_scan	Boolean, if ag = TRUE, should scan_ag be performed on predict_hyp output thus scanning only arabinogalactan motifs which contain predicted hydroxyprolines.
dom_sort	One of c("ievalue", "abc", "cba"), defaults to "ievalue". Domain plotting order. If 'ievalue' domains with the lowest ievalue as determined by hmmscan will be plotted above. If 'abc' or 'cba' the order is determined by domain Names.
progress	Boolean, whether to show the progress bar, at default set to FALSE.
gpi_size	Integer, the size of the gpi symbol. Appropriate values are 1 - 10.
gpi_shape	Integer, the shape of the gpi symbol. Appropriate values are 0 - 25
...	Appropriate arguments passed to get_signalp5, get_signalp, get_espritz, predict_hyp, get_hmm and scan_ag.

Value

A ggplot2 plot object

See Also

get_signalp5 get_signalp get_phobius get_tmhmm get_hmm get_cdd get_espritz predict_hyp scan_ag

Examples

library(ragp)
library(ggplot2)
ind <- c(23, 5, 80, 81, 345)
pred <- plot_prot(sequence = at_nsp$sequence[ind],
                  id = at_nsp$Transcript.id[ind])
pred +
  theme(legend.position = "bottom",
        legend.direction = "vertical")
        
#alternatively:      
nsp <- get_signalp(data = at_nsp[ind,],
                   id = Transcript.id,
                   sequence = sequence)
                    
hmm <- get_hmm(data = at_nsp[ind,], #default is to use get_cdd()
               id = Transcript.id,
               sequence = sequence) 
               
gpi <- get_netGPI(data = at_nsp[ind,],
                 id = Transcript.id,
                 sequence = sequence)                                    

tm <- get_phobius(data = at_nsp[ind,],
                  id = Transcript.id,
                  sequence = sequence)                                                        
 
disorder <- get_espritz(data = at_nsp[ind,],	
                        id = Transcript.id,	
                        sequence = sequence)
        
pred2 <- plot_prot(sequence = at_nsp$sequence[ind],
                   id = at_nsp$Transcript.id[ind],
                   tm = tm,
                   nsp = nsp,
                   gpi = gpi,
                   domain = hmm,
                   disorder = disorder)
                   
                   
pred2 +
  theme(legend.position = "bottom",
        legend.direction = "vertical")
        
#mixing both methods is also a possibility
        

missuse/ragp documentation built on Jan. 4, 2022, 10:49 a.m.