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

Description Usage Arguments Value Note Author(s) Examples

View source: R/plotCellMiner2D.R

Description

Make a simple 2d plot using two variables with ggplot2

Usage

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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

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## 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)

rcellminer documentation built on Nov. 26, 2020, 2:02 a.m.