@@ -16,6 +16,7 @@

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

 #' @param xLimVal a two entry vector (min, max) to set the x-axis

 #' @param yLimVal a two entry vector (min, max) to set the y-axis

+#' @param pointSize size of points on plot (DEFAULT: 3)

 #' 

 #' @note TROUBLESHOOTING NOTES: 1) Avoid ":" in colnames

 #' 

@@ -50,7 +51,7 @@

 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, singleColor="#0000FF",

-														alpha=1, numberColPrefix="X", xLimVal=NULL, yLimVal=NULL) {

+														alpha=1, numberColPrefix="X", xLimVal=NULL, yLimVal=NULL, pointSize=3) {

 	# nci60DrugActZ <- exprs(getAct(rcellminerData::drugData))

 	# nci60GeneExpZ <- getAllFeatureData(rcellminerData::molData)[["exp"]]

@@ -104,10 +105,10 @@ plotCellMiner2D <- function(df, xCol="x", yCol="y", xLabel=xCol, yLabel=yCol,

 	p1 <- p1 + theme_bw()

 	if(!is.null(colorPalette) && !is.null(classCol)) {

-		p1 <- p1 + suppressWarnings(geom_point(aes_string(color=classCol, text=tooltipCol), alpha=alpha, size = 3))

+		p1 <- p1 + suppressWarnings(geom_point(aes_string(color=classCol, text=tooltipCol), alpha=alpha, size = pointSize))

 		p1 <- p1 + scale_colour_manual(name="", values=colorPalette)

 	} else {

-		p1 <- p1 + suppressWarnings(geom_point(aes_string(text=tooltipCol), color=singleColor, alpha=alpha, size = 3))

+		p1 <- p1 + suppressWarnings(geom_point(aes_string(text=tooltipCol), color=singleColor, alpha=alpha, size = pointSize))

 	}

 	if(!is.null(xLabel)) {

@@ -22,7 +22,8 @@

 #' @importFrom rcdk view.image.2d

 rcdkplot <- function(molecule,width=300,height=300,marg=0,main='') {

 	par(mar=c(marg,marg,2.2,marg)) # set margins to zero since this isn't a real plot; top is 1.5 to accomodate title

-	temp1 <- view.image.2d(molecule,width,height) # get Java representation into an image matrix. set number of pixels you want horiz and vertical

+  depictor <- get.depictor(width=width, height=height) # Necessary as of Summer 2017

+	temp1 <- view.image.2d(molecule,depictor) # get Java representation into an image matrix. set number of pixels you want horiz and vertical

 	plot(NA,NA,xlim=c(1,10),ylim=c(1,10),xaxt='n',yaxt='n',xlab='',ylab='',main=main) # create an empty plot

 	rasterImage(temp1,1,1,10,10) # boundaries of raster: xmin, ymin, xmax, ymax. here i set them equal to plot boundaries

 }

\ No newline at end of file

@@ -17,7 +17,9 @@ specified along the rows, with rownames set appropriately.}

 \item{Z}{An N element  pattern specified as a vector or a k x N matrix of

 patterns specified along the rows. These are the patterns whose effect (with respect 

-to a linear model) is to be excluded when comparing x with Y or each row entry of Y.}

+to a linear model) is to be excluded when comparing x with Y or each row entry of Y.

+Note that for the partial correlation to be value, the pattern(s) in Z should 

+not overlap with those in x or Y.}

 \item{updateProgress}{A optional function to be invoked with each computed

 partial correlation to indicate progress.}

@@ -8,7 +8,7 @@ plotCellMiner2D(df, xCol = "x", yCol = "y", xLabel = xCol,

   yLabel = yCol, title = NULL, colorPalette = NULL, classCol = NULL,

   tooltipCol = NULL, showLegend = FALSE, showTrendLine = TRUE,

   showTitle = TRUE, singleColor = "#0000FF", alpha = 1,

-  numberColPrefix = "X", xLimVal = NULL, yLimVal = NULL)

+  numberColPrefix = "X", xLimVal = NULL, yLimVal = NULL, pointSize = 3)

 }

 \arguments{

 \item{df}{a data.frame with at least two columns}

@@ -42,6 +42,8 @@ plotCellMiner2D(df, xCol = "x", yCol = "y", xLabel = xCol,

 \item{xLimVal}{a two entry vector (min, max) to set the x-axis}

 \item{yLimVal}{a two entry vector (min, max) to set the y-axis}

+

+\item{pointSize}{size of points on plot (DEFAULT: 3)}

 }

 \value{

 a ggplot object