make_heatmap_vertical: Make a heatmap of masses split by fraction

In davidsbutcher/viztools: Innovative visualizations for top-down proteomics

Description

Uses a data frame containing mass and fraction columns to generate a heatmap showing the distribution of masses per fraction with a vertical orientation. DEPRECATED because make_heatmap() now supports vertical orientations.

Usage

make_heatmap_vertical(
  df,
  heatmapType = "Protein",
  binSize = 1000,
  savePDF = FALSE,
  outputDir = getwd(),
  pdfPrefix = format(Sys.time(), "%Y%m%d_%H%M%S"),
  massColname = "ObservedPrecursorMass",
  fractionColname = "fraction",
  Yrange = NULL,
  countRange = NULL
)

Arguments

df	A data frame containing columns for mass (in Daltons) and fraction.
heatmapType	Type of heatmap to create, typically "Protein" or "Proteoform".This only affects the legend title and output file name and can be any string.
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 in.
pdfPrefix	String to use to prepend heatmap names. Defaults to date and time.
massColname	Name of column containing masses. Defaults to "ObservedPrecursorMass".
fractionColname	Name of column containing fractions. Defaults to "fraction".
Yrange	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)

Examples

library(magrittr)

tibble::tibble(
   "fraction" =
      c(1,1,1,1,2,2,3,3,3,3),
   "ObservedPrecursorMass" =
      c(1500,3000,4200,4250,3500,4500,10500,12050,12075,14050)
) %>%
   make_heatmap(
      heatmapType = "Proteoform",
      savePDF = F,
      binSize = 500
   )

davidsbutcher/viztools documentation built on Oct. 5, 2020, 3:25 a.m.