Takes Coereba_MarkerExpressions data.frame and returns Marker Expression Beeswarm plots

Usage

Utility_MarkerPlots(
  data,
  panel,
  myfactor,
  shape_palette,
  fill_palette,
  cex = 1,
  size = 1.5,
  corral.width = 1,
  crossbar = "median",
  XAxisLevels = NULL,
  savePlot = FALSE,
  outpath = NULL,
  filename = NULL,
  dpi = 600,
  width = 9,
  height = 3,
  filterForThese = NULL,
  combinatorialStartsWith = NULL,
  style = "overlap"
)

Arguments

data: A data.frame of metadata and summarized markers from Utility_MarkerExpressions
panel: A .csv or data.frame containing Fluorophore and Marker columns of your panel markers.
myfactor: The column name by which you want to group outputs in the plot
shape_palette: A scale manual list assigning shape to factor level
fill_palette: A scale fill list assigning fill to factor level
cex: geom_beeswarm argument, default 1
size: geom_beeswarm argument, default 1.5
corral.width: geom_beeswarm argument, default 1
crossbar: geom_boxplot argument, default "median"
XAxisLevels: Provide list marker names correct order for x-axis reordering, default NULL
savePlot: Whether to save ggplot object to outfolder, default = FALSE
outpath: Specify file.path to desired storage location
filename: Specify desired filename
dpi: Specify desired pixel resolution
width: Specify desired width inches
height: Specify desired height inches
filterForThese: A list containing names of markers desire to include final plot, default NULL
combinatorialStartsWith: Default NULL, if aggregated data is combinatorial, starting string of characters (ex. CD45)
style: Default is "overlap", alternatively "separate" returns individual geom_boxplots

Value

Returns a ggplot object to R or designated Folder

Examples


shape_ptype <- c("HU" = 22, "HEU-lo" = 21, "HEU-hi" = 21)
fill_ptype <- c("HU" = "white", "HEU-lo" = "darkgray", "HEU-hi" = "black")

File_Location <- system.file("extdata", package = "Coereba")
panelPath <- file.path(File_Location, "ILTPanelTetramer.csv")
binaryPath <- file.path(File_Location, "HeatmapExample.csv")
dataPath <- file.path(File_Location, "ReadyFileExample.csv")
panelData <- read.csv(panelPath, check.names=FALSE)
binaryData <- read.csv(binaryPath, check.names=FALSE)
dataData <- read.csv(dataPath, check.names=FALSE)

All <- Coereba_MarkerExpressions(data=dataData, binary=binaryData,
 panel=panelData, starter="SparkBlue550")
#> Error in Coereba_MarkerExpressions(data = dataData, binary = binaryData,     panel = panelData, starter = "SparkBlue550"): unused arguments (data = dataData, binary = binaryData, panel = panelData, starter = "SparkBlue550")

ThePlot <- Utility_MarkerPlots(data=All, panel=panelData,
 myfactor="ptype", shape_palette = shape_ptype,
 fill_palette = fill_ptype, filterForThese=c("CD7", "CD4", "CD8"),
 XAxisLevels = c("CD7", "CD4", "CD8"))
#> Error: object 'All' not found