VolcanoPlot_Malignant_vs_normal

1. Load Libraries

2. Load Data

2.1 Load CSV Files with Mean Expression

# Load the CSV files with mean expression data
markers_mast_batch <- read.csv("1-MAST_with_batch_as_Covariate_with_meanExpression.csv", row.names = 1)

3. Volcano Plots for All Genes

3.1 Volcano Plot for MAST with Batch Correction

EnhancedVolcano(markers_mast_batch,
                lab = markers_mast_batch$gene,
                x = "avg_log2FC",
                y = "p_val_adj",
                title = "MAST with Batch Correction (All Genes)",
                pCutoff = 0.05,
                FCcutoff = 1.0)

Warning: One or more p-values is 0. Converting to 10^-1 * current lowest non-zero p-value...

3.2 Volcano Plot for MAST-Malignant vs Normal for patrticular genes

EnhancedVolcano(markers_mast_batch, 
                lab = markers_mast_batch$gene,
                x = "avg_log2FC", 
                y = "p_val_adj",
                selectLab = c('CDKN2A', 'CDKN1B', 'CDKN1A', 'MAPK14', 'MAPK1', 'NR2F1', 'SATB1', 'PDCD1', 'ZEB1', 'TP53', 'MKI67'),
                title = "Sézary CD4 T cells vs Normal CD4 T cells",
                xlab = bquote(~Log[2]~ 'fold change'),
                pCutoff = 0.01,
                FCcutoff = 1.5, 
                pointSize = 3.0,
                labSize = 3.0,
                boxedLabels = TRUE,
                colAlpha = 0.5,
                legendPosition = 'right',
                legendLabSize = 10,
                legendIconSize = 4.0,
                drawConnectors = TRUE,
                widthConnectors = 0.5,
                colConnectors = 'black',
                arrowheads = FALSE,
                max.overlaps = 30)

Warning: One or more p-values is 0. Converting to 10^-1 * current lowest non-zero p-value...