plotTrajectory.Rd
This function will plot a trajectory that was created onto an embedding.
plotTrajectory( ArchRProj = NULL, embedding = "UMAP", trajectory = "Trajectory", colorBy = "colData", name = "Trajectory", log2Norm = NULL, imputeWeights = if (!grepl("coldata", tolower(colorBy[1]))) getImputeWeights(ArchRProj), pal = NULL, size = 0.2, rastr = TRUE, quantCut = c(0.01, 0.99), quantHex = 0.5, discreteSet = NULL, continuousSet = NULL, randomize = TRUE, keepAxis = FALSE, baseSize = 6, addArrow = TRUE, plotAs = NULL, smoothWindow = 5, logFile = createLogFile("plotTrajectory"), ... )
ArchRProj | An |
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embedding | The name of the embedding to use to visualize the given |
trajectory | The column name in |
colorBy | A string indicating whether points in the plot should be colored by a column in |
name | The name of the column in |
log2Norm | A boolean value indicating whether a log2 transformation should be performed on the values from |
imputeWeights | The weights to be used for imputing numerical values for each cell as a linear combination of other cells'
values. See |
pal | The name of a custom palette from |
size | A number indicating the size of the points to plot if |
rastr | A boolean value that indicates whether the plot should be rasterized. This does not rasterize lines and labels, just the internal portions of the plot. |
quantCut | If this is not |
quantHex | The numeric xth quantile of all dots within each individual hexagon will determine the numerical value for
coloring to be displayed. This occurs when (i) |
discreteSet | The name of a discrete palette from |
continuousSet | The name of a continuous palette from |
randomize | A boolean value that indicates whether to randomize points prior to plotting to prevent cells from one cluster being present at the front of the plot. |
keepAxis | A boolean value that indicates whether the x and y axis ticks and labels should be plotted. |
baseSize | The base font size to use in the plot. |
addArrow | A boolean value that indicates whether to add a smoothed arrow in the embedding based on the aligned trajectory. |
plotAs | A string that indicates whether points ("points") should be plotted or a hexplot ("hex") should be plotted. By default
if |
smoothWindow | An integer value indicating the smoothing window for creating inferred Arrow overlay on to embedding. |
logFile | The path to a file to be used for logging ArchR output. |
... |