#' Make a simple 2d plot using two variables with ggplot2 
 #' 
 #' @param df a data.frame with at least two columns 

 #' @param xCol the name of the column in df with the "x" data. See Note
 #' @param yCol the name of the column in df with the "y" data. See Note
 #' @param xLabel the x plot label
 #' @param yLabel the y plot label
 #' @param title the plot title, if null the correlation will appear (DEFAULT: NULL)
 #' @param classCol the name of the column with the classes. Values in column of df must be a factor (DEFAULT: NULL)
 #' @param colorPalette a named vector with the names classes and value colors (DEFAULT: NULL)
 #' @param showLegend boolean, whether to show the legend (DEFAULT: FALSE)

 #' @param showTrendLine boolean, whether to show the trendline 

 #' @param showTitle boolean, whether to show the title
 #' @param alpha value from 0-1, where 0 indicates transparent points

 #' @param numberColPrefix a prefix to add to column names that start with a number that causes issues with ggplot (DEFAULT: X)

 #' 
 #' @return a ggplot object
 #' 
 #' @examples
 #' \dontrun{
 #' # Load data
 #' nci60DrugActZ <- exprs(getAct(rcellminerData::drugData))
 #' nci60GeneExpZ <- getAllFeatureData(rcellminerData::molData)[["exp"]]
 #' # Load colors
 #' colorTab <- loadNciColorSet(returnDf=TRUE)
 #' tissueColorTab <- unique(colorTab[, c("tissues", "colors")])
 #' # Merge data
 #' df <- as.data.frame(t(rbind(nci60DrugActZ["94600",], nci60GeneExpZ["SLFN11",])))
 #' colnames(df) <- c("y", "x")
 #' df <- cbind(df, colorTab)
 #' # Plot data

 #' plotCellMiner2D(df, xCol="x", yCol="y", xLabel="SLFN11", yLabel="94600")

 #' plotCellMiner2D(df, xCol="x", yCol="y", showTrendLine = FALSE, showTitle = FALSE)
 #' plotCellMiner2D(df, xCol="x", yCol="y", showTrendLine = FALSE, showLegend = FALSE)
 #' }
 #' 
 #' @author Augustin Luna <augustin AT mail.nih.gov>
 #' 

 #' @note Uses ggplot aes_string() which uses parse() to turn your text expression into a proper R symbol that can be resolved within the data.frame. Avoid numbers and spaces in 
 #' 
 #' @importFrom ggplot2 ggplot geom_point theme_bw scale_colour_manual xlab ylab geom_smooth ggtitle theme aes_string

 #' 
 #' @concept rcellminer
 #' @export

 plotCellMiner2D <- function(df, xCol="x", yCol="y", xLabel=xCol, yLabel=yCol, 
 														title=NULL, colorPalette=NULL, classCol=NULL, tooltipCol=NULL, 
 														showLegend=FALSE, showTrendLine=TRUE, showTitle=TRUE, 

 														alpha=1, numberColPrefix="X") {

 	
 	# nci60DrugActZ <- exprs(getAct(rcellminerData::drugData))
 	# nci60GeneExpZ <- getAllFeatureData(rcellminerData::molData)[["exp"]]
 	# # Load colors
 	# colorTab <- loadNciColorSet(returnDf=TRUE)
 	# tissueColorTab <- unique(colorTab[, c("tissues", "colors")])
 	# # Merge data
 	# xCol <- "SLFN11"
 	# yCol <- "94600"
 	# classCol <- "tissues"
 	# xLabel <- xCol
 	# yLabel <- yCol
 	# title <- NULL
 	# df <- data.frame(y=nci60DrugActZ[yCol,], x=nci60GeneExpZ[xCol,])
 	# yCol <- "X94600" # MUST NOT BE A NUMBER
 	# colnames(df) <- c(yCol, xCol)
 	# df <- cbind(df, colorTab)
 	# df[, classCol] <- as.factor(df[, classCol])
 	# colorPalette <- tissueColorTab[, "colors"]
 	# names(colorPalette) <- tissueColorTab[, classCol]
 	# colors <- rep("blue", nrow(df))
 	# colors[1:10, "colors"] <- "red"
 	# showLegend <- FALSE
 	# showTrendLine <- TRUE
 	# showTitle <- TRUE
 	# alpha <- 1
 	

 	# Fix column names if they start with a number 
 	if (grepl("^[0-9]", xCol)) {
 		tmpXCol <- paste0(numberColPrefix, xCol)
 		df[, tmpXCol] <- df[, xCol]
 		xCol <- tmpXCol
 	}
 
 	if (grepl("^[0-9]", yCol)) {
 		tmpYCol <- paste0(numberColPrefix, yCol)
 		df[, tmpYCol] <- df[, yCol]
 		yCol <- tmpYCol
 	}
 
 	# Create title 

 	if(is.null(title)) {
 		corResults <- cor.test(df[,xCol], df[,yCol], use="pairwise.complete.obs")

 		title <- paste0(paste(yLabel, '~', xLabel),

 										', r=', round(corResults$estimate, 2),
 										' p=', signif(corResults$p.value, 2))
 	}
 
 	# Plot image
 	p1 <- ggplot(data=df, aes_string(x=xCol, y=yCol))
 	p1 <- p1 + theme_bw()
 	

 	if(!is.null(colorPalette) && !is.null(classCol)) {
 		p1 <- p1 + geom_point(aes_string(color=classCol, text=tooltipCol), alpha=alpha)
 		p1 <- p1 + scale_colour_manual(name="", values=colorPalette)
 	} else {
 		p1 <- p1 + geom_point(aes_string(text=tooltipCol), color="#0000FF", alpha=alpha)

 	}
 

 	if(!is.null(xLabel)) {
 		p1 <- p1 + xlab(xLabel)		

 	} else {
 		p1 <- p1 + xlab(xCol)				
 	}
 

 	if(!is.null(yLabel)) {
 		p1 <- p1 + ylab(yLabel)		

 	} else {
 		p1 <- p1 + ylab(yCol)				
 	}
 	
 	if(showTrendLine) {
 		p1 <- p1 + geom_smooth(method = "lm", se = FALSE, color = "red")
 	}
 	
 	if(showTitle) {
 		p1 <- p1 + ggtitle(title)
 	}
 	
 	if(!showLegend) {
 		p1 <- p1 + theme(legend.position="none")
 	}
 	
 	return(p1)

 }