Enhanced Visualization of Gene Presence in Luise_Sepi_STKN

1. prepare typing_ST2_until_QPB07837.csv (under DIR ~/DATA/Data_Luise_Sepi_STKN/plotTreeHeatmap_mibi_isolates and ENV r_env)

   cp ../presence_absence_ST2/QPB*.fasta ./
   cp ../plotTreeHeatmap/typing.csv ./typing_until_QPB07571.csv
   
   # -- makeblastdb --
   #for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do
   #    makeblastdb -in ../shovill/${sample}/contigs.fa -dbtype nucl
   #done
   
   for i in {572..622}; do
       id_1=$(printf "QPB07%03d" "$((i-1))")
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do"
           echo "blastn -db ../shovill/\${sample}/contigs.fa -query ${id}.fasta -evalue 1e-40 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   done
   
   for i in {572..622}; do
       id_1=$(printf "QPB07%03d" "$((i-1))")
       id=$(printf "QPB07%03d" "$i")
       echo "python ~/Scripts/process_directory.py ${id} typing_until_${id_1}.csv typing_until_${id}.csv"
   done
   
   #reprace all '+' with 'MT880870' in typing_until_QPB07622.csv
   sed -i 's/+/MT880870/g' typing_until_QPB07622.csv
   

2. prepare typing_until_QPB07667.csv

   for i in {623..667}; do
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do"
           echo "blastn -db ../shovill/\${sample}/contigs.fa -query ${id}.fasta -evalue 1e-40 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   done
   
   for i in {623..667}; do
       id_1=$(printf "QPB07%03d" "$((i-1))")
       id=$(printf "QPB07%03d" "$i")
       echo "python ~/Scripts/process_directory.py ${id} typing_until_${id_1}.csv typing_until_${id}.csv"
   done
   
   sed -i 's/+/MT880871/g' typing_until_QPB07667.csv
   

3. prepare typing_until_QPB07667.csv

   for i in {668..750}; do
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do"
           echo "blastn -db ../shovill/\${sample}/contigs.fa -query ${id}.fasta -evalue 1e-40 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   done
   
   for i in {751..837}; do
       id=$(printf "QPB07%03d" "$i")
       echo "mkdir ${id}"
       echo "for sample in mibi1435 mibi1436 mibi1437 mibi1438 mibi1439 mibi1440 mibi1441 mibi1442 mibi1443 mibi1444 mibi1445 mibi1446 mibi1447 mibi1448 mibi1449 mibi1450 mibi1451 mibi1452 mibi1453 mibi1454 mibi1455 mibi1456 mibi1457 mibi1458 mibi1459 mibi1460 mibi1461 mibi1462 mibi1463 mibi1464 mibi1465 mibi1466 mibi1467 mibi1468 mibi1469 mibi1471 mibi1473 mibi1474 mibi1475 mibi1476 mibi1477 mibi1478 mibi1479 mibi1480 mibi1481 mibi1482 mibi1483 mibi1484 mibi1485 mibi1486 mibi1487 mibi1488 mibi1489 mibi1490 mibi1491 mibi1492 mibi1493 mibi1494 mibi1495 mibi1496 mibi1497 mibi1498 mibi1499 mibi1500 mibi1501 mibi1502 mibi1503 mibi1504 mibi1505 mibi1506 mibi2312 mibi2313 mibi2314 mibi2315 mibi2316 mibi2317 mibi2318 mibi2319 mibi2320 mibi2321 mibi2379; do"
           echo "blastn -db ../shovill/\${sample}/contigs.fa -query ${id}.fasta -evalue 1e-40 -num_threads 15 -outfmt 6 -strand both -max_target_seqs 1 > ./${id}/\${sample}.blastn"
       echo "done"
   done
   
   for i in {668..837}; do
       id_1=$(printf "QPB07%03d" "$((i-1))")
       id=$(printf "QPB07%03d" "$i")
       echo "python ~/Scripts/process_directory.py ${id} typing_until_${id_1}.csv typing_until_${id}.csv"
   done
   
   sed -i 's/+/MT880872/g' typing_until_QPB07837.csv
   
   cut -d$'\t' -f1-43 typing_until_QPB07837.csv > temp1
   cut -d$'\t' -f44- typing_until_QPB07837.csv > temp2
   
   sed -i 's/MT880870/+/g' temp1
   paste -d$'\t' temp1 temp2 > ggtree_and_gheatmap_mibi_phages.csv
   

4. plot tree heatmap under /mnt/md1/DATA_md1/Data_Luise_Sepi_STKN/plotTreeHeatmap_mibi_isolates

   cp ../plotTreeHeatmap/990_backup.tree ./
   
   library(ggtree)
   library(ggplot2)
   library(dplyr)
   setwd("/home/jhuang/DATA/Data_Luise_Sepi_STKN/plotTreeHeatmap_mibi_isolates/")
   # -- edit tree --
   #https://icytree.org/
   #0.000780
   
   # -- for the figure ggtree_and_gheatmap_mibi_phages.png --
   info <- read.csv("ggtree_and_gheatmap_mibi.csv", sep="\t")
   info$name <- info$Isolate
   tree <- read.tree("990_backup.tree")
   cols <- c("2"="cornflowerblue","5"="darkgreen","7"="seagreen3","9"="tan","14"="red",  "17"="navyblue", "23"="gold",     "35"="green","59"="orange","73"="pink","81"="purple","86"="magenta","87"="brown", "89"="darksalmon","130"="chocolate4","190"="darkkhaki", "290"="azure3", "297"="maroon","325"="lightgreen",     "454"="blue","487"="cyan", "558"="skyblue2", "766"="blueviolet")
   #cols <- c("2"='purple2', "other"='darksalmon')  #purple2  skyblue2
   heatmapData2 <- info %>% select(Isolate,  QPB07572, QPB07573, QPB07574, QPB07575, QPB07576, QPB07577, QPB07578, QPB07579, QPB07580, QPB07581, QPB07582, QPB07583, QPB07584, QPB07585, QPB07586, QPB07587, QPB07588, QPB07589, QPB07590, QPB07591, QPB07592, QPB07593, QPB07594, QPB07595, QPB07596, QPB07597, QPB07598, QPB07599, QPB07600, QPB07601, QPB07602, QPB07603, QPB07604, QPB07605, QPB07606, QPB07607, QPB07608, QPB07609, QPB07610, QPB07611, QPB07612, QPB07613, QPB07614, QPB07615, QPB07616, QPB07617, QPB07618, QPB07619, QPB07620, QPB07621, QPB07622, QPB07623, QPB07624, QPB07625, QPB07626, QPB07627, QPB07628, QPB07629, QPB07630, QPB07631, QPB07632, QPB07633, QPB07634, QPB07635, QPB07636, QPB07637, QPB07638, QPB07639, QPB07640, QPB07641, QPB07642, QPB07643, QPB07644, QPB07645, QPB07646, QPB07647, QPB07648, QPB07649, QPB07650, QPB07651, QPB07652, QPB07653, QPB07654, QPB07655, QPB07656, QPB07657, QPB07658, QPB07659, QPB07660, QPB07661, QPB07662, QPB07663, QPB07664, QPB07665, QPB07666, QPB07667, QPB07668, QPB07669, QPB07670, QPB07671, QPB07672, QPB07673, QPB07674, QPB07675, QPB07676, QPB07677, QPB07678, QPB07679, QPB07680, QPB07681, QPB07682, QPB07683, QPB07684, QPB07685, QPB07686, QPB07687, QPB07688, QPB07689, QPB07690, QPB07691, QPB07692, QPB07693, QPB07694, QPB07695, QPB07696, QPB07697, QPB07698, QPB07699, QPB07700, QPB07701, QPB07702, QPB07703, QPB07704, QPB07705, QPB07706, QPB07707, QPB07708, QPB07709, QPB07710, QPB07711, QPB07712, QPB07713, QPB07714, QPB07715, QPB07716, QPB07717, QPB07718, QPB07719, QPB07720, QPB07721, QPB07722, QPB07723, QPB07724, QPB07725, QPB07726, QPB07727, QPB07728, QPB07729, QPB07730, QPB07731, QPB07732, QPB07733, QPB07734, QPB07735, QPB07736, QPB07737, QPB07738, QPB07739, QPB07740, QPB07741, QPB07742, QPB07743, QPB07744, QPB07745, QPB07746, QPB07747, QPB07748, QPB07749, QPB07750, QPB07751, QPB07752, QPB07753, QPB07754, QPB07755, QPB07756, QPB07757, QPB07758, QPB07759, QPB07760, QPB07761, QPB07762, QPB07763, QPB07764, QPB07765, QPB07766, QPB07767, QPB07768, QPB07769, QPB07770, QPB07771, QPB07772, QPB07773, QPB07774, QPB07775, QPB07776, QPB07777, QPB07778, QPB07779, QPB07780, QPB07781, QPB07782, QPB07783, QPB07784, QPB07785, QPB07786, QPB07787, QPB07788, QPB07789, QPB07790, QPB07791, QPB07792, QPB07793, QPB07794, QPB07795, QPB07796, QPB07797, QPB07798, QPB07799, QPB07800, QPB07801, QPB07802, QPB07803, QPB07804, QPB07805, QPB07806, QPB07807, QPB07808, QPB07809, QPB07810, QPB07811, QPB07812, QPB07813, QPB07814, QPB07815, QPB07816, QPB07817, QPB07818, QPB07819, QPB07820, QPB07821, QPB07822, QPB07823, QPB07824, QPB07825, QPB07826, QPB07827, QPB07828, QPB07829, QPB07830, QPB07831, QPB07832, QPB07833, QPB07834, QPB07835, QPB07836, QPB07837)  #ST,
   rn <- heatmapData2$Isolate
   heatmapData2$Isolate <- NULL
   heatmapData2 <- as.data.frame(sapply(heatmapData2, as.character))
   rownames(heatmapData2) <- rn
   
   heatmap.colours <- c("darkred", "darkblue", "darkgreen", "grey")
   names(heatmap.colours) <- c("MT880870","MT880871","MT880872","-")
   
   #heatmap.colours <- c("cornflowerblue","darkgreen","seagreen3","tan","red",  "navyblue", "gold",     "green","orange","pink","purple","magenta","brown", "darksalmon","chocolate4","darkkhaki", "azure3", "maroon","lightgreen",     "blue","cyan", "skyblue2", "blueviolet",       "darkred", "darkblue", "darkgreen", "grey")
   #names(heatmap.colours) <- c("2","5","7","9","14", "17","23",   "35","59","73", "81","86","87","89","130","190","290", "297","325",    "454","487","558","766",       "MT880870","MT880871","MT880872","-")
   
   #mydat$Regulation <- factor(mydat$Regulation, levels=c("up","down"))
   #circular
   
   p <- ggtree(tree, layout='circular', branch.length='none') %<+% info + geom_tippoint(aes(color=ST)) + scale_color_manual(values=cols) + geom_tiplab2(aes(label=name), offset=1)
   png("ggtree.png", width=1260, height=1260)
   #svg("ggtree.svg", width=1260, height=1260)
   p
   dev.off()
   
   #gheatmap(p, heatmapData2, width=0.1, colnames_position="top", colnames_angle=90, colnames_offset_y = 0.1, hjust=0.5, font.size=4, offset = 5) + scale_fill_manual(values=heatmap.colours) +  theme(legend.text = element_text(size = 14)) + theme(legend.title = element_text(size = 14)) + guides(fill=guide_legend(title=""), color = guide_legend(override.aes = list(size = 5)))
   
   png("ggtree_and_gheatmap_mibi_phages.png", width=1290, height=1000)
   #svg("ggtree_and_gheatmap_mibi_phages.svg", width=17, height=15)
   gheatmap(p, heatmapData2, width=0.5, colnames_position="top", colnames_angle=90, colnames_offset_y = 0.1, hjust=0.5, font.size=0, offset = 6) + scale_fill_manual(values=heatmap.colours) +  theme(legend.text = element_text(size = 16)) + theme(legend.title = element_text(size = 16)) + guides(fill=guide_legend(title=""), color = guide_legend(override.aes = list(size = 5)))
   dev.off()
   
   # -- for the figure ggtree_and_gheatmap_mibi_selected_genes.png --
   
   info <- read.csv("ggtree_and_gheatmap_mibi.csv", sep="\t")
   info$name <- info$Isolate
   tree <- read.tree("990_backup.tree")
   cols <- c("2"="cornflowerblue","5"="darkgreen","7"="seagreen3","9"="tan","14"="red",  "17"="navyblue", "23"="gold",     "35"="green","59"="orange","73"="pink","81"="purple","86"="magenta","87"="brown", "89"="darksalmon","130"="chocolate4","190"="darkkhaki", "290"="azure3", "297"="maroon","325"="lightgreen",     "454"="blue","487"="cyan", "558"="skyblue2", "766"="blueviolet")
   
   heatmapData2 <- info %>% select(Isolate,       SCCmec,  agr.typing,      gyrB,    fumC,    gltA,    icd,     apsS,    sigB,    sarA,    agrC,    yycG,    psm.β,   psm.δ,   hlb,     atlE,    atl,     sdrG,    sdrH,    ebh,     ebpS,    tagB,    capC,    sepA,    dltA,    fmtC,    lipA,    sceD,    SE0760,  esp,     ecpA)  #ST,
   rn <- heatmapData2$Isolate
   heatmapData2$Isolate <- NULL
   heatmapData2 <- as.data.frame(sapply(heatmapData2, as.character))
   rownames(heatmapData2) <- rn
   
   #heatmap.colours <- c("darkred", "darkblue", "darkgreen", "grey")
   #names(heatmap.colours) <- c("MT880870","MT880871","MT880872","-")
   
   #heatmap.colours <- c("cornflowerblue","darkgreen","seagreen3","tan","red",  "navyblue", "gold",     "green","orange","pink","purple","magenta","brown", "darksalmon","chocolate4","darkkhaki", "azure3", "maroon","lightgreen",     "blue","cyan", "skyblue2", "blueviolet",       "darkred", "darkblue", "darkgreen", "grey")
   #names(heatmap.colours) <- c("2","5","7","9","14", "17","23",   "35","59","73", "81","86","87","89","130","190","290", "297","325",    "454","487","558","766",       "MT880870","MT880871","MT880872","-")
   
   heatmap.colours <- c("cornflowerblue","darkgreen","seagreen3","tan","red",  "navyblue", "purple",     "green","cyan",       "darkred", "darkblue", "darkgreen", "grey",  "darkgreen", "grey")
   names(heatmap.colours) <- c("SCCmec_type_II(2A)", "SCCmec_type_III(3A)", "SCCmec_type_III(3A) and SCCmec_type_VIII(4A)", "SCCmec_type_IV(2B)", "SCCmec_type_IV(2B&5)", "SCCmec_type_IV(2B) and SCCmec_type_VI(4B)", "SCCmec_type_IVa(2B)", "SCCmec_type_IVb(2B)", "SCCmec_type_IVg(2B)",  "I", "II", "III", "none", "+","-")
   
   #mydat$Regulation <- factor(mydat$Regulation, levels=c("up","down"))
   #circular
   
   p <- ggtree(tree, layout='circular', branch.length='none') %<+% info + geom_tippoint(aes(color=ST)) + scale_color_manual(values=cols) + geom_tiplab2(aes(label=name), offset=1)
   png("ggtree.png", width=1260, height=1260)
   #svg("ggtree.svg", width=1260, height=1260)
   p
   dev.off()
   
   #gheatmap(p, heatmapData2, width=0.1, colnames_position="top", colnames_angle=90, colnames_offset_y = 0.1, hjust=0.5, font.size=4, offset = 5) + scale_fill_manual(values=heatmap.colours) +  theme(legend.text = element_text(size = 14)) + theme(legend.title = element_text(size = 14)) + guides(fill=guide_legend(title=""), color = guide_legend(override.aes = list(size = 5)))
   
   png("ggtree_and_gheatmap_mibi_selected_genes.png", width=1590, height=1300)
   #svg("ggtree_and_gheatmap_mibi_selected_genes.svg", width=17, height=15)
   gheatmap(p, heatmapData2, width=2, colnames_position="top", colnames_angle=90, colnames_offset_y = 2.0, hjust=0.7, font.size=4, offset = 8) + scale_fill_manual(values=heatmap.colours) +  theme(legend.text = element_text(size = 16)) + theme(legend.title = element_text(size = 16)) + guides(fill=guide_legend(title=""), color = guide_legend(override.aes = list(size = 5)))
   dev.off()
   

5. Report

   I’ve attached a figure (ggtree_and_gheatmap_mibi_selected_genes.png) that illustrates the presence and absence of the selected genes. This is a visual representation of the table I sent to you earlier. The presence or absence of each gene in the corresponding genomes was determined using a BLASTn comparison between the genome and the gene sequences.
   
   Additionally, I’ve updated the figure ggtree_and_gheatmap_mibi_phages.png. In this new version, all ST types are represented in distinct colors. The raw data for both figures can be found in the attached Excel file (ggtree_and_gheatmap_mibi.xlsx).
   

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