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name: bio-flow-cytometry-differential-analysis description: Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups. tool_type: r primary_tool: CATALYST

Differential Analysis

Differential Abundance (DA)

Copylibrary(CATALYST)
library(diffcyt)

# Load clustered data
sce <- readRDS('sce_clustered.rds')

# Create design matrix
design <- createDesignMatrix(ei(sce), cols_design = 'condition')

# Create contrast
contrast <- createContrast(c(0, 1))  # Treatment vs Control

# Differential abundance test
res_DA <- testDA_edgeR(sce, design, contrast, cluster_id = 'meta20')

# View results
rowData(res_DA)$cluster_id
rowData(res_DA)$p_adj

# Significant clusters
sig_DA <- rowData(res_DA)$p_adj < 0.05
table(sig_DA)

Differential State (DS)

Copy# Test for marker expression differences within clusters
res_DS <- testDS_limma(sce, design, contrast,
                        cluster_id = 'meta20',
                        markers_include = rownames(sce)[rowData(sce)$marker_class == 'state'])

# Results per marker per cluster
ds_results <- rowData(res_DS)

Visualization

Copy# DA results heatmap
plotDiffHeatmap(sce, res_DA, all = TRUE, fdr = 0.05)

# DS results heatmap
plotDiffHeatmap(sce, res_DS, all = TRUE, fdr = 0.05)

# Abundance by condition
plotAbundances(sce, k = 'meta20', by = 'cluster_id', group_by = 'condition')

Manual Statistical Testing

Copylibrary(tidyverse)

# Get cluster frequencies per sample
freqs <- colData(sce) %>%
    as.data.frame() %>%
    group_by(sample_id, condition, cluster_id = cluster_ids(sce, 'meta20')) %>%
    summarise(n = n(), .groups = 'drop') %>%
    group_by(sample_id) %>%
    mutate(freq = n / sum(n) * 100)

# Test each cluster
test_abundance <- function(df, cluster) {
    cluster_data <- filter(df, cluster_id == cluster)
    ctrl <- filter(cluster_data, condition == 'Control')$freq
    treat <- filter(cluster_data, condition == 'Treatment')$freq

    if (length(ctrl) >= 2 && length(treat) >= 2) {
        test <- t.test(treat, ctrl)
        return(data.frame(
            cluster = cluster,
            fc = mean(treat) / mean(ctrl),
            pvalue = test$p.value
        ))
    }
    return(NULL)
}

results <- map_dfr(unique(freqs$cluster_id), ~test_abundance(freqs, .x))
results$padj <- p.adjust(results$pvalue, method = 'BH')

Mixed Effects Models

Copylibrary(lme4)
library(lmerTest)

# For paired/repeated measures designs
# Random effect for patient/donor

fit_mixed <- function(df, cluster) {
    cluster_data <- filter(df, cluster_id == cluster)

    model <- lmer(freq ~ condition + (1|patient_id), data = cluster_data)

    coef <- summary(model)$coefficients
    return(data.frame(
        cluster = cluster,
        estimate = coef[2, 'Estimate'],
        pvalue = coef[2, 'Pr(>|t|)']
    ))
}

CITRUS (Automated Discovery)

Copylibrary(citrus)

# Prepare data
fcs_files <- list.files('data', pattern = '\\.fcs$', full.names = TRUE)
labels <- c(rep('Control', 2), rep('Treatment', 2))

# Run CITRUS
citrus_result <- citrus(
    fcs_files,
    labels,
    fileSampleSize = 1000,
    featureType = 'abundances',
    modelType = 'glmnet',
    family = 'classification'
)

# Get significant clusters
citrus_plot(citrus_result)

Volcano Plot

Copylibrary(ggplot2)

# From DA results
da_df <- as.data.frame(rowData(res_DA))
da_df$significant <- da_df$p_adj < 0.05

ggplot(da_df, aes(x = logFC, y = -log10(p_adj), color = significant)) +
    geom_point() +
    geom_hline(yintercept = -log10(0.05), linetype = 'dashed') +
    geom_vline(xintercept = c(-1, 1), linetype = 'dashed') +
    scale_color_manual(values = c('gray', 'red')) +
    theme_bw() +
    labs(title = 'Differential Abundance')

Export Results

Copy# Combine DA and DS results
da_results <- as.data.frame(rowData(res_DA))
da_results$analysis <- 'DA'

ds_results <- as.data.frame(rowData(res_DS))
ds_results$analysis <- 'DS'

# Save
write.csv(da_results, 'da_results.csv', row.names = FALSE)
write.csv(ds_results, 'ds_results.csv', row.names = FALSE)

Multiple Comparisons

Copy# For multiple conditions
design_full <- model.matrix(~ 0 + condition, data = ei(sce))
colnames(design_full) <- levels(factor(ei(sce)$condition))

# Multiple contrasts
contrasts <- makeContrasts(
    TreatA_vs_Ctrl = TreatmentA - Control,
    TreatB_vs_Ctrl = TreatmentB - Control,
    TreatA_vs_B = TreatmentA - TreatmentB,
    levels = design_full
)

# Test each contrast
res_list <- lapply(1:ncol(contrasts), function(i) {
    testDA_edgeR(sce, design_full, contrasts[, i], cluster_id = 'meta20')
})

Related Skills

• clustering-phenotyping - Cluster data first
• gating-analysis - Compare gated populations
• differential-expression - Similar statistical concepts