plotCellMiner2D {rcellminer} | R Documentation |
Make a simple 2d plot using two variables with ggplot2
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, pointSize = 3 )
df |
a data.frame with at least two columns |
xCol |
the name of the column in df with the "x" data. See Note |
yCol |
the name of the column in df with the "y" data. See Note |
xLabel |
the x plot label |
yLabel |
the y plot label |
title |
the plot title, if null the correlation will appear (DEFAULT: NULL) |
colorPalette |
a named vector with the names classes and value colors (DEFAULT: NULL) |
classCol |
the name of the column with the classes. Values in column of df must be a factor (DEFAULT: NULL) |
tooltipCol |
the name of the column used for tooltips when plotted with plotly |
showLegend |
boolean, whether to show the legend (DEFAULT: FALSE) |
showTrendLine |
boolean, whether to show the trendline |
showTitle |
boolean, whether to show the title |
singleColor |
a color to be used for all points when a color palette is not provided (DEFAULT: blue) |
alpha |
value from 0-1, where 0 indicates transparent points (DEFAULT: 1, not transparent) |
numberColPrefix |
a prefix to add to column names that start with a number that causes issues with ggplot (DEFAULT: X) |
xLimVal |
a two entry vector (min, max) to set the x-axis |
yLimVal |
a two entry vector (min, max) to set the y-axis |
pointSize |
size of points on plot (DEFAULT: 3) |
a ggplot object
TROUBLESHOOTING NOTES: 1) Avoid ":" in colnames
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
Augustin Luna <augustin AT mail.nih.gov>
## Not run: # 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) ## End(Not run)