Make a heatmap of masses split by fraction

Uses a data frame containing mass and fraction columns to generate a heatmap showing the distribution of masses per fraction.

make_heatmap(
  df,
  plotType = "Protein",
  orientation = "h",
  binSize = 1000,
  savePDF = FALSE,
  outputDir = getwd(),
  outputPrefix = format(Sys.time(), "%Y%m%d_%H%M%S"),
  massColname = "mass",
  fractionColname = "fraction",
  axisRange = NULL,
  countRange = NULL
)

Arguments

df	A data frame containing columns for mass (in Daltons) and fraction.
plotType	Type of heatmap to create, typically "Protein" or "Proteoform".This only affects the legend title and output file name and can be any string.
orientation	Controls orientation of heatmap. Set to "h" for horizontal (mass bins on X-axis) or "v" for vertical.
binSize	Size of the mass bin in Daltons. Masses in the data frame should be in Daltons.
savePDF	Boolean value (TRUE or FALSE). Should a PDF be saved to the output directory?
outputDir	Directory to place output files into.
outputPrefix	String to use to prepend heatmap output filenames. Defaults to date and time.
massColname	Name of column containing masses. Defaults to "mass".
fractionColname	Name of column containing fractions. Defaults to "fraction".
axisRange	Numeric vector of length 2 specifying range of heatmap in kDa. Defaults to NULL, and range is determined by rounding highest mass bin up to the nearest interval of 5.
countRange	Numeric vector of length 2 specifying range of counts to use for generating heatmap fill color range. Defaults to NULL, which determines color range automatically using ggplot2::scale_fill_viridis_c(option = "C", direction = -1). Useful for creating multiple heatmaps with matching fill color ranges.

Value

A heatmap (a ggplot object)

Examples

df <-
   data.frame(
      "fraction" =
         c(1,1,1,1,2,2,3,3,3,3),
      "mass" =
         c(1500,3000,4200,4250,3500,4500,10500,12050,12075,14050)
   )

   make_heatmap(
      df,
      plotType = "Protein",
      savePDF = F,
      binSize = 1000
   )