UniformClusters | R Documentation |
This group of functions takes in input a COTAN
object and
handle the task of dividing the dataset into Uniform Clusters, that is
clusters that have an homogeneous genes' expression. This condition is
checked by calculating the GDI
of the cluster and verifying that no
more than a small fraction of the genes have their GDI
level above the
given GDIThreshold
GDIPlot(
objCOTAN,
genes,
condition = "",
statType = "S",
GDIThreshold = 1.43,
GDIIn = NULL
)
cellsUniformClustering(
objCOTAN,
GDIThreshold = 1.43,
cores = 1L,
maxIterations = 25L,
optimizeForSpeed = TRUE,
deviceStr = "cuda",
initialClusters = NULL,
initialResolution = 0.8,
useDEA = TRUE,
distance = NULL,
hclustMethod = "ward.D2",
saveObj = TRUE,
outDir = "."
)
checkClusterUniformity(
objCOTAN,
clusterName,
cells,
GDIThreshold = 1.43,
cores = 1L,
optimizeForSpeed = TRUE,
deviceStr = "cuda",
saveObj = TRUE,
outDir = "."
)
mergeUniformCellsClusters(
objCOTAN,
clusters = NULL,
GDIThreshold = 1.43,
batchSize = 0L,
notMergeable = NULL,
cores = 1L,
optimizeForSpeed = TRUE,
deviceStr = "cuda",
useDEA = TRUE,
distance = NULL,
hclustMethod = "ward.D2",
saveObj = TRUE,
outDir = "."
)
objCOTAN |
a |
genes |
a named |
condition |
a string corresponding to the condition/sample (it is used only for the title). |
statType |
type of statistic to be used. Default is "S": Pearson's chi-squared test statistics. "G" is G-test statistics |
GDIThreshold |
the threshold level that discriminates uniform clusters.
It defaults to |
GDIIn |
when the |
cores |
number of cores to use. Default is 1. |
maxIterations |
max number of re-clustering iterations. It defaults to
|
optimizeForSpeed |
Boolean; when |
deviceStr |
On the |
initialClusters |
an existing clusterization to use as starting point: the clusters deemed uniform will be kept and the rest processed as normal |
initialResolution |
a number indicating how refined are the clusters
before checking for uniformity. It defaults to |
useDEA |
Boolean indicating whether to use the DEA to define the distance; alternatively it will use the average Zero-One counts, that is faster but less precise. |
distance |
type of distance to use. Default is |
hclustMethod |
It defaults is |
saveObj |
Boolean flag; when |
outDir |
an existing directory for the analysis output. The effective output will be paced in a sub-folder. |
clusterName |
the tag of the cluster |
cells |
the cells belonging to the cluster |
clusters |
The clusterization to merge. If not given the last available clusterization will be used, as it is probably the most significant! |
batchSize |
Number pairs to test in a single round. If none of them
succeeds the merge stops. Defaults to |
notMergeable |
An array of names of merged clusters that are already known for not being uniform. Useful to restart the merging process after an interruption. |
GDIPlot()
directly evaluates and plots the GDI
for a sample.
cellsUniformClustering()
finds a Uniform clusterizations by
means of the GDI
. Once a preliminary clusterization is obtained from
the Seurat-package
methods, each cluster is checked for uniformity
via the function checkClusterUniformity()
. Once all clusters are
checked, all cells from the non-uniform clusters are pooled together
for another iteration of the entire process, until all clusters are
deemed uniform. In the case only a few cells are left out (\leq
50
), those are flagged as "-1"
and the process is stopped.
checkClusterUniformity()
takes a COTAN
object and a cells'
cluster and checks whether the latter is uniform by GDI
. The
function runs COTAN
to check whether the GDI
is lower than the given
GDIThreshold
for the 99\%
of the genes. If the GDI
results to be
too high for too many genes, the cluster is deemed non-uniform.
mergeUniformCellsClusters()
takes in a uniform
clusterization and iteratively checks whether merging two near clusters
would form a uniform cluster still. This function uses the cosine
distance to establish the nearest clusters pairs. It will use the
checkClusterUniformity()
function to check whether the merged clusters
are uniform. The function will stop once no near pairs of clusters
are mergeable in a single batch
GDIPlot()
returns a ggplot2
object
cellsUniformClustering()
returns a list
with 2 elements:
"clusters"
the newly found cluster labels array
"coex"
the associated COEX
data.frame
checkClusterUniformity
returns a list with:
"isUniform"
: a flag indicating whether the cluster is uniform
"fractionAbove"
: the percentage of genes with GDI
above the threshold
"firstPercentile"
: the quantile associated to the highest percentile
"size"
: the number of cells in the cluster
a list
with:
"clusters"
the merged cluster labels array
"coex"
the associated COEX
data.frame
data("test.dataset")
objCOTAN <- automaticCOTANObjectCreation(raw = test.dataset,
GEO = "S",
sequencingMethod = "10X",
sampleCondition = "Test",
cores = 6L,
saveObj = FALSE)
groupMarkers <- list(G1 = c("g-000010", "g-000020", "g-000030"),
G2 = c("g-000300", "g-000330"),
G3 = c("g-000510", "g-000530", "g-000550",
"g-000570", "g-000590"))
gdiPlot <- GDIPlot(objCOTAN, genes = groupMarkers, cond = "test")
plot(gdiPlot)
## Here we override the default GDI threshold as a way to speed-up
## calculations as higher threshold implies less stringent uniformity
## It real applications it might be appropriate to change the threshold
## in cases of relatively low genes/cells number, or in cases when an
## rough clusterization is needed in the early satges of the analysis
##
splitList <- cellsUniformClustering(objCOTAN, cores = 6L,
optimizeForSpeed = TRUE,
deviceStr = "cuda",
initialResolution = 0.8,
GDIThreshold = 1.46, saveObj = FALSE)
clusters <- splitList[["clusters"]]
firstCluster <- getCells(objCOTAN)[clusters %in% clusters[[1L]]]
firstClusterIsUniform <-
checkClusterUniformity(objCOTAN, GDIThreshold = 1.46,
cluster = clusters[[1L]], cells = firstCluster,
cores = 6L, optimizeForSpeed = TRUE,
deviceStr = "cuda", saveObj = FALSE)[["isUniform"]]
objCOTAN <- addClusterization(objCOTAN,
clName = "split",
clusters = clusters)
objCOTAN <- addClusterizationCoex(objCOTAN,
clName = "split",
coexDF = splitList[["coex"]])
identical(reorderClusterization(objCOTAN)[["clusters"]], clusters)
mergedList <- mergeUniformCellsClusters(objCOTAN,
GDIThreshold = 1.46,
batchSize = 5L,
clusters = clusters,
cores = 6L,
optimizeForSpeed = TRUE,
deviceStr = "cpu",
distance = "cosine",
hclustMethod = "ward.D2",
saveObj = FALSE)
objCOTAN <- addClusterization(objCOTAN,
clName = "merged",
clusters = mergedList[["clusters"]],
coexDF = mergedList[["coex"]])
identical(reorderClusterization(objCOTAN), mergedList)
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