hgate_sample: hgate_sample

In ebecht/hypergate: Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry

hgate_sample

Description

Downsample the data in order to fasten the computation and reduce the memory usage.

Usage

hgate_sample(gate_vector, level, size = 1000, method = "prop")

Arguments

gate_vector	A Categorical vector whose length equals the number of rows of the matrix to sample (nrow(xp))
level	A level of gate_vector so that gate_vector == level will produce a boolean vector identifying events of interest
size	An integer specifying the maximum number of events of interest to retain. If the count of events of interest is lower than size, than size will be set to that count.
method	A string specifying the method to balance the count of events. "prop" means proportionnality: if events of interest are sampled in a 1/10 ratio, then all others events are sampled by the same ratio. "10x" means a balance of 10 between the count events of interest and the count all others events. "ceil" means a uniform sampling no more than the specified size for each level of the gate_vector. level is unused in that method.

Value

A logical vector with TRUE correspond to the events being sampled, ie kept to further analysis

Note

No replacement is applied. If there are less events in one group or the alternate than the algorithm requires, then all available events are returned. NA values in gate_vector are not sampled, ie ignored.

Examples

# Standard procedure with downsampling
data(Samusik_01_subset)
xp <- Samusik_01_subset$xp_src[,Samusik_01_subset$regular_channels]
gate_vector <- Samusik_01_subset$labels
sampled <- hgate_sample(gate_vector, level=8, 100)
table(sampled)
table(gate_vector[sampled])
xp_sampled <- xp[sampled, ]
gate_vector_sampled <- gate_vector[sampled]
hg <- hypergate(xp_sampled, gate_vector_sampled, level=8, delta_add=0.01)
# cluster 8 consists in 122 events
table(gate_vector)
# Downsampling
table(gate_vector[hgate_sample(gate_vector, level=8, 100)])
# Downsampling reduces the alternate events
table(gate_vector[hgate_sample(gate_vector, level=8, 100, "10x")])
# Downsampling is limited to the maximum number of events of interest
table(gate_vector[hgate_sample(gate_vector, level=8, 150)])
# Downsampling is limited to the maximum number of events of interest, and
# the alternate events are downsampled to a total of 10 times
table(gate_vector[hgate_sample(gate_vector, level=8, 150, "10x")])
# More details about sampling
# Convert -1 to NA, NA are not sampled
gate_vector[gate_vector==-1] = NA
gate_vector = factor(gate_vector)
table(gate_vector, useNA = "alw")
#
# target size = 100 whereas initial freq is 122 for pop 8
smp.prop = hgate_sample(gate_vector, level = 8, size = 100, method = "prop")
smp.10x  = hgate_sample(gate_vector, level = 8, size = 100, method = "10x")
smp.ceil = hgate_sample(gate_vector, size = 10, method = "ceil")
table(smp.prop)
table(smp.10x)
table(smp.ceil)
rbind(raw = table(gate_vector),
      prop = table(gate_vector[smp.prop]),
      `10x` = table(gate_vector[smp.10x]),
      ceil = table(gate_vector[smp.ceil]))
#
# target size = 30 whereas initial freq is 25 for pop 14
smp.prop = hgate_sample(gate_vector, level = 14, size = 30, method = "prop")
smp.10x  = hgate_sample(gate_vector, level = 14, size = 30, method = "10x")
table(smp.prop)
table(smp.10x)
rbind(raw = table(gate_vector),
      prop = table(gate_vector[smp.prop]),
      `10x` = table(gate_vector[smp.10x]))
# prop returns original data, because target size ids larger than initial freq
# 10x  returns sampled data according to initial freq, such as the total amount
# of other events equals 10x initial freq of pop 14

ebecht/hypergate documentation built on Feb. 4, 2024, 3:29 p.m.