VolcanoPlot_L1_vs_L2_MAST with RNA and SCT assay

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-L1_vs_L2_SCT_MAST.csv", row.names = 1)

markers_mast_batch2 <- read.csv("2-L1_vs_L2_SCT_MAST_clusters.csv", row.names = 1)

markers_mast_batch3 <- read.csv("3-L1_vs_L2_RNA_MAST_clusters.csv", row.names = 1)

3. Volcano Plots for All Genes

3.1 Volcano Plot for L1_vs_L2_SCT_MAST_using_cell_lines

EnhancedVolcano(markers_mast_batch,
                lab = rownames(markers_mast_batch),
                x = "avg_log2FC",
                y = "p_val_adj",
                title = "L1_vs_L2_SCT_MAST_using_cell_lines",
                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 L1_vs_L2_SCT_MAST_using_cell_lines

EnhancedVolcano(markers_mast_batch, 
                lab = rownames(markers_mast_batch),
                x = "avg_log2FC", 
                y = "p_val_adj",
                selectLab = c('EPCAM', 'KIR3DL2', 'FOXM1', 'TWIST1', 'TNFSF9', 
                              'CD80', 'FOS','PTPN6','NCR1','NCR2',
                              'PCLAF', 'KIR3DL1', 'IL4','ITGA6','CCL5',
                              'IL7R', 'TCF7', 'PTTG1', 'RRM2', 'MKI67', 'CD70', 
                              'IL2RA', 'FCGR3A', 'GNLY', 'FOXP3', 'SELL',  'LEF1',
                              'CCL17', 'THY1', 'CD27', 'CD28', 'CD7',
                              # Key Sézary syndrome genes
                              'PRF1', 'GZMB', 'NCR1', 'NFATC3', 
                              'KLRK1', 'LCK', 'KLRC1', 'KLRC2', 'TNF', 
                              'KIR3DL1','KIR3DL3','KIR3DL4', 'IFNG', 'IFNGR1', 'CD244', 'FASLG'),
                title = "L1_vs_L2_SCT_MAST_using_cell_lines",
                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...

4. Volcano Plots for All Genes

4.1 Volcano Plot for MAST with Batch Correction

EnhancedVolcano(markers_mast_batch2,
                lab = rownames(markers_mast_batch2),
                x = "avg_log2FC",
                y = "p_val_adj",
                title = "L1_vs_L2_SCT_MAST_using_clusters",
                pCutoff = 0.05,
                FCcutoff = 1.0)

4.2 Volcano Plot for L1_vs_L2_SCT_MAST_using_clusters

EnhancedVolcano(markers_mast_batch2, 
                lab = rownames(markers_mast_batch2),
                x = "avg_log2FC", 
                y = "p_val_adj",
                selectLab = c('EPCAM', 'KIR3DL2', 'FOXM1', 'TWIST1', 'TNFSF9', 
                              'CD80', 'FOS','PTPN6','NCR1','NCR2',
                              'PCLAF', 'KIR3DL1', 'IL4','ITGA6','CCL5',
                              'IL7R', 'TCF7', 'PTTG1', 'RRM2', 'MKI67', 'CD70', 
                              'IL2RA', 'FCGR3A', 'GNLY', 'FOXP3', 'SELL',  'LEF1',
                              'CCL17', 'THY1', 'CD27', 'CD28', 'CD7',
                              # Key Sézary syndrome genes
                              'PRF1', 'GZMB', 'NCR1', 'NFATC3', 
                              'KLRK1', 'LCK', 'KLRC1', 'KLRC2', 'TNF', 
                              'KIR3DL1','KIR3DL3','KIR3DL4', 'IFNG', 'IFNGR1', 'CD244', 'FASLG'),
                title = "L1_vs_L2_SCT_MAST_using_clusters",
                xlab = bquote(~Log[2]~ 'fold change'),
                pCutoff = 0.01,
                FCcutoff = 1, 
                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)

5. Volcano Plots for All Genes

5.1 Volcano Plot for L1_vs_L2_RNA_MAST_using_clusters

EnhancedVolcano(markers_mast_batch3,
                lab = rownames(markers_mast_batch3),
                x = "avg_log2FC",
                y = "p_val_adj",
                title = "L1_vs_L2_RNA_MAST_using_clusters",
                pCutoff = 0.05,
                FCcutoff = 1.0)

5.2 Volcano Plot for L1_vs_L2_RNA_MAST_using_clusters

EnhancedVolcano(markers_mast_batch3, 
                lab = rownames(markers_mast_batch3),
                x = "avg_log2FC", 
                y = "p_val_adj",
                selectLab = c('EPCAM', 'KIR3DL2', 'FOXM1', 'TWIST1', 'TNFSF9', 
                              'CD80', 'FOS','PTPN6','NCR1','NCR2',
                              'PCLAF', 'KIR3DL1', 'IL4','ITGA6','CCL5',
                              'IL7R', 'TCF7', 'PTTG1', 'RRM2', 'MKI67', 'CD70', 
                              'IL2RA', 'FCGR3A', 'GNLY', 'FOXP3', 'SELL',  'LEF1',
                              'CCL17', 'THY1', 'CD27', 'CD28', 'CD7',
                              # Key Sézary syndrome genes
                              'PRF1', 'GZMB', 'NCR1', 'NFATC3', 
                              'KLRK1', 'LCK', 'KLRC1', 'KLRC2', 'TNF', 
                              'KIR3DL1','KIR3DL3','KIR3DL4', 'IFNG', 'IFNGR1', 'CD244', 'FASLG'),
                title = "L1_vs_L2_RNA_MAST_using_clusters",
                xlab = bquote(~Log[2]~ 'fold change'),
                pCutoff = 0.01,
                FCcutoff = 1, 
                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)