1. rcellminer
  2. Commit 2e57538244cd845d594575db8d25f7109b0bc514
Browse code

Added a parameter/fix for column names that start with numbers (e.g. NSCs) that are not liked by ggplot

cannin authored on 27/02/2017 16:27:34
Showing 2 changed files
R/plotCellMiner2D.R
History View file @ 2e57538
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@@ -12,6 +12,7 @@
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 #' @param showTrendLine boolean, whether to show the trendline
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 #' @param showTitle boolean, whether to show the title
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 #' @param alpha value from 0-1, where 0 indicates transparent points
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+#' @param numberColPrefix a prefix to add to column names that start with a number that causes issues with ggplot (DEFAULT: X)
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 #'
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 #' @return a ggplot object
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 #'
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@@ -44,7 +45,7 @@
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 plotCellMiner2D <- function(df, xCol="x", yCol="y", xLabel=xCol, yLabel=yCol,
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 														title=NULL, colorPalette=NULL, classCol=NULL, tooltipCol=NULL,
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 														showLegend=FALSE, showTrendLine=TRUE, showTitle=TRUE,
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-														alpha=1) {
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+														alpha=1, numberColPrefix="X") {
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 	# nci60DrugActZ <- exprs(getAct(rcellminerData::drugData))
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 	# nci60GeneExpZ <- getAllFeatureData(rcellminerData::molData)[["exp"]]
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@@ -72,6 +73,20 @@ plotCellMiner2D <- function(df, xCol="x", yCol="y", xLabel=xCol, yLabel=yCol,
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 	# showTitle <- TRUE
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 	# alpha <- 1
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+	# Fix column names if they start with a number
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+	if (grepl("^[0-9]", xCol)) {
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+		tmpXCol <- paste0(numberColPrefix, xCol)
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+		df[, tmpXCol] <- df[, xCol]
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+		xCol <- tmpXCol
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+	}
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+
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+	if (grepl("^[0-9]", yCol)) {
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+		tmpYCol <- paste0(numberColPrefix, yCol)
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+		df[, tmpYCol] <- df[, yCol]
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+		yCol <- tmpYCol
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+	}
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+
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+	# Create title
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 	if(is.null(title)) {
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 		corResults <- cor.test(df[,xCol], df[,yCol], use="pairwise.complete.obs")
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 		title <- paste0(paste(yLabel, '~', xLabel),
man/plotCellMiner2D.Rd
History View file @ 2e57538
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@@ -7,7 +7,7 @@
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 plotCellMiner2D(df, xCol = "x", yCol = "y", xLabel = xCol,
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   yLabel = yCol, title = NULL, colorPalette = NULL, classCol = NULL,
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   tooltipCol = NULL, showLegend = FALSE, showTrendLine = TRUE,
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-  showTitle = TRUE, alpha = 1)
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+  showTitle = TRUE, alpha = 1, numberColPrefix = "X")
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 }
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 \arguments{
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 \item{df}{a data.frame with at least two columns}
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@@ -33,6 +33,8 @@ plotCellMiner2D(df, xCol = "x", yCol = "y", xLabel = xCol,
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 \item{showTitle}{boolean, whether to show the title}
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 \item{alpha}{value from 0-1, where 0 indicates transparent points}
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+
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+\item{numberColPrefix}{a prefix to add to column names that start with a number that causes issues with ggplot (DEFAULT: X)}
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 }
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 \value{
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 a ggplot object