plotInfiltrationDensity: Plot and print absolute density or density percentages of...

Description Usage Arguments Value

View source: R/plots.R

Description

Plot and print absolute density or density percentages of cell types near tumor interface

Usage

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plotInfiltrationDensity(mDen, densityMarkers, bandWidth, clrs, plotTitle = "",
  cellTypeLabels = NULL, sampleOrder = NULL, yMax = NULL,
  separateLegend = FALSE, printLegend = TRUE, legendOnly = FALSE,
  yCol = "Density", pct = FALSE, facetByFOV = TRUE,
  facetByCellType = FALSE, yAxisTitle = "Density (counts/mm^2)",
  xAxisTitle = "Distance to Tumor Interface")

Arguments

mDen

tibble containing

densityMarkers

a vector of markers for which density is to be plotted

bandWidth

if plotting by distance intervals from infiltration boundary, this is the size of each interval

clrs

a list of colors, named by either by CellType from mDen tibble, or cellTypeLabels if specified

plotTitle

title of plot

cellTypeLabels

a list of labels for each marker being plotted, if different than CellType in mDen tibble; default: NULL

sampleOrder

order in which samples should appear on the plot; default=NULL

yMax

if specified, y axis will span from zero to this number; default=NULL

separateLegend

logical; when TRUE, legend will be separated from plot. if printLegend is TRUE, will be printed first, before plot. if printLegend is FALSE, will not be printed at all; default=FALSE

printLegend

logical; when separateLegend is TRUE, if printLegend is FALSE, no legend will be printed at all; default=TRUE

legendOnly

logical; when separateLegend is TRUE, if legendOnly is TRUE, only legend will be printed, no plot

yCol

character string specifying which of the columns in mDen is to be used for y values; default="Density"

pct

logical; values being plotted are percentages; default=FALSE

facetByFOV

logical; plot each FOV separately; default=TRUE

facetByCellType

logical; plot each cell type separately; default=FALSE

yAxisTitle

character string to be used as title of the y axis

xAxisTitle

character string to be used as title of the x axis

Value

nothing


caitlinjones/halo documentation built on May 7, 2019, 8 a.m.