#' Connect and parse UniProt information.
#'
#' This function can be used to get a list of UniProt Accession/s from a csv file.
#'
#' @usage PlotPhysicochemical(SeqDataObjPath , directorypath = NULL)
#'
#' @param SeqDataObjPath Dataframe returned from GetSequence function.
#'
#' @param directorypath Path to save Physcochemical properties plot.
#'
#' @author Mohmed Soudy \email{Mohamed.soudy@57357.com} and Ali Mostafa \email{ali.mo.anwar@std.agr.cu.edu.eg}
#'
#' @export
PlotPhysicochemical <- function(SeqDataObjPath , directorypath = NULL)
{
seqdata <- select(SeqDataObjPath , "Sequence")
result = aminoAcidProperties(seqdata , seq="Sequence")
#Group data frame by charge
ChargeGroup <- rep("Negative" , dim(result)[1])
positive_index <- which(result$Sequence_aa_charge > 0)
ChargeGroup[positive_index] <- "Positive"
result <- cbind(result , ChargeGroup)
#Get charge Sign ratios
Chargecount <- table(sign(result$Sequence_aa_charge))
if (length(Chargecount) == 1){
Chargecount <- as.table(cbind(Chargecount , 0));
}
Chargeratio <- table(sign(result$Sequence_aa_charge))/dim(result)[1]*100
if (length(Chargeratio) == 1){
Chargeratio <- as.table(cbind(Chargeratio , 0));
}
#Construct Charge dataframe
Chargedf = data.frame(x = c("Negative" , "Positive") , y = Chargeratio , z = Chargecount)
#Group data frame by GRAVY charge
GravyGroup <- rep("Negative" , dim(result)[1])
positive_index <- which(result$Sequence_aa_gravy > 0)
GravyGroup[positive_index] <- "Positive"
result <- cbind(result , GravyGroup)
#Get GRAVY sign ratios
GRAVYcount <- table(sign(result$Sequence_aa_gravy))
if (length(GRAVYcount) == 1){
GRAVYcount <- as.table(cbind(GRAVYcount , 0));
}
GRAVYratio <- table(sign(result$Sequence_aa_gravy))/dim(result)[1]*100
if (length(GRAVYratio) == 1){
GRAVYratio <- as.table(cbind(GRAVYratio , 0));
}
#Construct GRAVY dataframe
GRAVYdf = data.frame(x = c("Negative" , "Positive") , y = GRAVYratio , z = GRAVYcount)
#Charge plot
Chargebarplot <- ggplot(result, aes(x=as.numeric(reorder(rownames(result) , result$Sequence_aa_charge)), y=result$Sequence_aa_charge, label=rownames(result))) +
geom_bar(stat='identity', aes(fill=result$ChargeGroup)) + theme_classic() + theme(axis.title.x = element_blank() , axis.ticks.x = element_blank() , plot.title = element_text(hjust = 0.5))+ylab("Protein charge")+
guides(fill=guide_legend(title="Groups"))+ggtitle("Sequence Charge") + scale_x_continuous(limits = c(0, dim(result)[1]), expand = c(0, 0))
Chargebarplot
Chargeframeplot <- ggplot(Chargedf , aes(x = Chargedf$x , y = Chargedf$z.Freq))+
geom_bar(stat = "identity" , aes(fill = Chargedf$y.Freq)) + geom_text(aes(label = paste0(as.character(round(Chargedf$y.Freq),2), "%")) , size = 4, vjust = -1)+theme_bw()+
theme(legend.position = "none" , plot.title = element_text(hjust = 0.5))+xlab("Groups") + ylab("Protein count") + ggtitle("Sequence Charge") + scale_y_continuous(limits = c(0, dim(result)[1]), expand = c(0, 1))
Chargeframeplot
#GRAVY plot
GRAVYbarplot <- ggplot(result, aes(x=as.numeric(reorder(rownames(result), result$Sequence_aa_gravy)), y=result$Sequence_aa_gravy, label=rownames(result))) +
geom_bar(stat='identity', aes(fill=result$GravyGroup)) + theme_classic() + theme(axis.title.x = element_blank() , axis.ticks.x = element_blank() , plot.title = element_text(hjust = 0.5))+ylab("GRAVY index")+
guides(fill=guide_legend(title="Groups"))+ggtitle("Sequence GRAVY index") + scale_x_continuous(limits = c(0, dim(result)[1]), expand = c(0, 0))
GRAVYbarplot
GRAVYframeplot <- ggplot(GRAVYdf , aes(x = GRAVYdf$x , y = GRAVYdf$z.Freq))+
geom_bar(stat = "identity" , aes(fill = GRAVYdf$y.Freq)) + geom_text(aes(label = paste0(as.character(round(GRAVYdf$y.Freq),2), "%")) , size = 4, vjust = -0.6)+theme_bw()+
theme(legend.position = "none" , plot.title = element_text(hjust = 0.5))+xlab("Groups") + ylab("Protein count") + ggtitle("GRAVY index") + scale_y_continuous(limits = c(0, dim(result)[1]), expand = c(0, 1))
GRAVYframeplot
Allplot <- ggarrange(Chargebarplot , Chargeframeplot , GRAVYbarplot , GRAVYframeplot , nrow = 2 , ncol = 2, align = "hv")
Allplot
#Plot acidic vs Basic Groups
AcidicBasic <- c(result$Sequence_aa_acidic , result$Sequence_aa_basic)
AcidicBasicGroup <- rep("Acidic" , length(result$Sequence_aa_acidic))
AcidicBasicGroup <- c(AcidicBasicGroup , rep("Basic" , length(result$Sequence_aa_basic)))
AcidicBasicframe <- data.frame(x = AcidicBasic , y = AcidicBasicGroup)
p<-ggplot(AcidicBasicframe, aes(x=AcidicBasicframe$y, y=AcidicBasicframe$x, fill=AcidicBasicframe$y)) +
geom_violin(alpha = 0.3)+ geom_boxplot(width=0.1) +
guides(fill=guide_legend(title="Groups"))+ xlab("Groups") + ylab("Hydrophobicity")+
theme_bw() + ggtitle("Hydrophobicity") + theme(plot.title = element_text(hjust = 0.5))
p
TestAll <- ggarrange(Allplot , p , ncol = 2 , nrow = 1)
plot(TestAll)
if (!is.null(directorypath))
{
ggsave(filename =paste0(directorypath , "//" , "Physochemical.jpeg") , plot = TestAll , device = "jpeg" , width = 15 , height = 8 , dpi = 320)
ggsave(filename =paste0(directorypath , "//" , "Physochemical.tiff") , plot = TestAll , device = "tiff" , width = 15 , height = 8 , dpi = 320)
}
}
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