plotCellMiner2D: Make a simple 2d plot using two variables with ggplot2

In cannin/rcellminer: rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

Make a simple 2d plot using two variables with ggplot2

Description

Make a simple 2d plot using two variables with ggplot2

Usage

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
)

Arguments

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)

Value

a ggplot object

Note

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

Author(s)

Augustin Luna <augustin AT mail.nih.gov>

Examples

## 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)

cannin/rcellminer documentation built on Aug. 11, 2024, 8:45 a.m.