Description Usage Arguments Value
Plot and print absolute density or density percentages of cell types near tumor interface
1 2 3 4 5 6 | 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")
|
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 |
nothing
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