plotMarkerHeatmap | R Documentation |
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,
subsetMarkers = NULL,
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. |
plotLog2FC |
A boolean value that indicates whether the |
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. |
subsetMarkers |
A vector of rownames from seMarker to use for subsetting of seMarker to only plot specific features on the heatmap.
Note that these rownames are expected to be integers that come from |
labelMarkers |
A character vector listing the |
nLabel |
An integer value that indicates how many of 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. |
#Get Test Project
proj <- getTestProject()
#Get Markers
seMarker <- getMarkerFeatures(
ArchRProj = proj,
useMatrix = "PeakMatrix",
testMethod = "binomial",
binarize = TRUE
)
#Plot Markers
p <- plotMarkerHeatmap(seMarker)
#PDF
plotPDF(p, name = "Marker-Heatmap", ArchRProj = proj)
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