plotMarkerHeatmap.Rd
This function will plot a heatmap of the results from markerFeatures
plotMarkerHeatmap( seMarker = NULL, cutOff = "FDR <= 0.01 & Log2FC >= 0.5", log2Norm = TRUE, scaleTo = 10^4, scaleRows = TRUE, plotLog2FC = FALSE, limits = c(-2, 2), grepExclude = NULL, pal = NULL, binaryClusterRows = TRUE, clusterCols = TRUE, labelMarkers = NULL, nLabel = 15, nPrint = 15, labelRows = FALSE, returnMatrix = FALSE, transpose = FALSE, invert = FALSE, logFile = createLogFile("plotMarkerHeatmap") )
seMarker | A |
---|---|
cutOff | A valid-syntax logical statement that defines which marker features from |
log2Norm | A boolean value indicating whether a log2 transformation should be performed on the values in
|
scaleTo | Each column in the assay Mean from |
scaleRows | A boolean value that indicates whether the heatmap should display row-wise z-scores instead of raw values. |
limits | A numeric vector of two numbers that represent the lower and upper limits of the heatmap color scheme. |
grepExclude | A character vector or string that indicates the |
pal | A custom continuous palette from |
binaryClusterRows | A boolean value that indicates whether a binary sorting algorithm should be used for fast clustering of heatmap rows. |
clusterCols | A boolean value that indicates whether the columns of the marker heatmap should be clustered. |
labelMarkers | A character vector listing the |
nLabel | An integer value that indicates whether the top |
nPrint | If provided |
labelRows | A boolean value that indicates whether all rows should be labeled on the side of the heatmap. |
returnMatrix | A boolean value that indicates whether the final heatmap matrix should be returned in lieu of plotting the actual heatmap. |
transpose | A boolean value that indicates whether the heatmap should be transposed prior to plotting or returning. |
invert | A boolean value that indicates whether the heatmap will display the features with the
lowest |
logFile | The path to a file to be used for logging ArchR output. |