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3group-analysis
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# Untreated-direct killing comparisons
percentages <-GetFeatures(fsom = fsom_untreated,
files = paste0(dir_u_prep, files_untreated),
type = "percentages")
# Low-moderate comparison
groups.ud3.l.m <- list("Low-killing" = paste0(dir_u_prep, files_untreated[c(2,3,5,6)]),
"Moderate-killing" = paste0(dir_u_prep, files_untreated[c(4,8)]))
MC_stats.ud3.lm <- GroupStats(percentages[["metacluster_percentages"]], groups.ud3.l.m)
C_stats.ud3.lm <- GroupStats(percentages[["cluster_percentages"]], groups.ud3.l.m)
fold_changes.ud3.lm <- C_stats.ud3.lm["fold changes", ]
fold_changes.ud3.lm <- factor(ifelse(fold_changes.ud3.lm < -1, "Underrepresented compared to low killing group",
ifelse(fold_changes.ud3.lm > 1, "Overrepresented compared to low killing group",
"--")), levels = c("--", "Underrepresented compared to low killing group",
"Overrepresented compared to low killing group"))
fold_changes.ud3.lm[is.na(fold_changes.ud3.lm)] <- "--"
sbs.ud3.low <- PlotStars(fsom_untreated, title = "Low killing donors",
nodeSizes = C_stats.ud3.lm["medians Low-killing", ],
refNodeSize = max(C_stats.ud3.lm[c("medians Low-killing", "medians Moderate-killing"),]),
backgroundValues = fold_changes.ud3.lm,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
sbs.ud3.mod <- PlotStars(fsom_untreated, title = "Moderate killing donors",
nodeSizes = C_stats.ud3.lm["medians Moderate-killing", ],
refNodeSize = max(C_stats.ud3.lm[c("medians Low-killing", "medians Moderate-killing"),]),
backgroundValues = fold_changes.ud3.lm,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
untreateddirect3.lm <- ggpubr::ggarrange(plotlist = list(sbs.ud3.low$tree, sbs.ud3.mod$tree,
sbs.ud3.mod$starLegend, sbs.ud3.mod$backgroundLegend),
ncol = 2, nrow = 2,
heights = c(4, 1))
# Low-high comparison
groups.ud3.l.h <- list("Low-killing" = paste0(dir_u_prep, files_untreated[c(2,3,5,6)]),
"High-killing" = paste0(dir_u_prep, files_untreated[c(7,9)]))
MC_stats.ud3.lh <- GroupStats(percentages[["metacluster_percentages"]], groups.ud3.l.h)
C_stats.ud3.lh <- GroupStats(percentages[["cluster_percentages"]], groups.ud3.l.h)
fold_changes.ud3.lh <- C_stats.ud3.lh["fold changes", ]
fold_changes.ud3.lh <- factor(ifelse(fold_changes.ud3.lh < -1, "Underrepresented compared to low killing group",
ifelse(fold_changes.ud3.lh > 1, "Overrepresented compared to low killing group",
"--")), levels = c("--", "Underrepresented compared to low killing group",
"Overrepresented compared to low killing group"))
fold_changes.ud3.lh[is.na(fold_changes.ud3.lh)] <- "--"
sbs.ud3.low <- PlotStars(fsom_untreated, title = "Low killing donors",
nodeSizes = C_stats.ud3.lh["medians Low-killing", ],
refNodeSize = max(C_stats.ud3.lh[c("medians Low-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.lh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
sbs.ud3.high <- PlotStars(fsom_untreated, title = "High killing donors",
nodeSizes = C_stats.ud3.lh["medians High-killing", ],
refNodeSize = max(C_stats.ud3.lh[c("medians Low-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.lh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
untreateddirect3.lh <- ggpubr::ggarrange(plotlist = list(sbs.ud3.low$tree, sbs.ud3.high$tree,
sbs.ud3.high$starLegend, sbs.ud3.high$backgroundLegend),
ncol = 2, nrow = 2,
heights = c(4, 1))
# Moderate-high comparison
groups.ud3.m.h <- list("Moderate-killing" = paste0(dir_u_prep, files_untreated[c(4,8)]),
"High-killing" = paste0(dir_u_prep, files_untreated[c(7,9)]))
MC_stats.ud3.mh <- GroupStats(percentages[["metacluster_percentages"]], groups.ud3.m.h)
C_stats.ud3.mh <- GroupStats(percentages[["cluster_percentages"]], groups.ud3.m.h)
fold_changes.ud3.mh <- C_stats.ud3.mh["fold changes", ]
fold_changes.ud3.mh <- factor(ifelse(fold_changes.ud3.mh < -1, "Underrepresented compared to moderate killing group",
ifelse(fold_changes.ud3.mh > 1, "Overrepresented compared to moderate killing group",
"--")), levels = c("--", "Underrepresented compared to moderate killing group",
"Overrepresented compared to moderate killing group"))
fold_changes.ud3.mh[is.na(fold_changes.ud3.mh)] <- "--"
sbs.ud3.mod <- PlotStars(fsom_untreated, title = "Moderate killing donors",
nodeSizes = C_stats.ud3.mh["medians Moderate-killing", ],
refNodeSize = max(C_stats.ud3.mh[c("medians Moderate-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.mh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
sbs.ud3.high <- PlotStars(fsom_untreated, title = "High killing donors",
nodeSizes = C_stats.ud3.mh["medians High-killing", ],
refNodeSize = max(C_stats.ud3.mh[c("medians Moderate-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.mh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
untreateddirect3.mh <- ggpubr::ggarrange(plotlist = list(sbs.ud3.mod$tree, sbs.ud3.high$tree,
sbs.ud3.high$starLegend, sbs.ud3.high$backgroundLegend),
ncol = 2, nrow = 2,
heights = c(4, 1))
# Print all 3 comparisons per condition
pdf("C:/Users/Me/OneDrive - University of Nebraska at Omaha/Administrative/Documents/FUSE 2023/PhenoData/Untreated/results/untreated_direct3_tree.pdf")
untreateddirect3.lm
untreateddirect3.lh
untreateddirect3.mh
dev.off()
# Untreated-ADCC killing comparisons
percentages <-GetFeatures(fsom = fsom_untreated,
files = paste0(dir_u_prep, files_untreated),
type = "percentages")
# Low-moderate comparison
groups.ud3.l.m <- list("Low-killing" = paste0(dir_u_prep, files_untreated[c(5,6)]),
"Moderate-killing" = paste0(dir_u_prep, files_untreated[c(1:4,7)]))
MC_stats.ud3.lm <- GroupStats(percentages[["metacluster_percentages"]], groups.ud3.l.m)
C_stats.ud3.lm <- GroupStats(percentages[["cluster_percentages"]], groups.ud3.l.m)
fold_changes.ud3.lm <- C_stats.ud3.lm["fold changes", ]
fold_changes.ud3.lm <- factor(ifelse(fold_changes.ud3.lm < -1, "Underrepresented compared to low killing group",
ifelse(fold_changes.ud3.lm > 1, "Overrepresented compared to low killing group",
"--")), levels = c("--", "Underrepresented compared to low killing group",
"Overrepresented compared to low killing group"))
fold_changes.ud3.lm[is.na(fold_changes.ud3.lm)] <- "--"
sbs.ud3.low <- PlotStars(fsom_untreated, title = "Low killing donors",
nodeSizes = C_stats.ud3.lm["medians Low-killing", ],
refNodeSize = max(C_stats.ud3.lm[c("medians Low-killing", "medians Moderate-killing"),]),
backgroundValues = fold_changes.ud3.lm,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
sbs.ud3.mod <- PlotStars(fsom_untreated, title = "Moderate killing donors",
nodeSizes = C_stats.ud3.lm["medians Moderate-killing", ],
refNodeSize = max(C_stats.ud3.lm[c("medians Low-killing", "medians Moderate-killing"),]),
backgroundValues = fold_changes.ud3.lm,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
untreateddirect3.lm <- ggpubr::ggarrange(plotlist = list(sbs.ud3.low$tree, sbs.ud3.mod$tree,
sbs.ud3.mod$starLegend, sbs.ud3.mod$backgroundLegend),
ncol = 2, nrow = 2,
heights = c(4, 1))
# Low-high comparison
groups.ud3.l.h <- list("Low-killing" = paste0(dir_u_prep, files_untreated[c(5,6)]),
"High-killing" = paste0(dir_u_prep, files_untreated[c(8,9)]))
MC_stats.ud3.lh <- GroupStats(percentages[["metacluster_percentages"]], groups.ud3.l.h)
C_stats.ud3.lh <- GroupStats(percentages[["cluster_percentages"]], groups.ud3.l.h)
fold_changes.ud3.lh <- C_stats.ud3.lh["fold changes", ]
fold_changes.ud3.lh <- factor(ifelse(fold_changes.ud3.lh < -1, "Underrepresented compared to low killing group",
ifelse(fold_changes.ud3.lh > 1, "Overrepresented compared to low killing group",
"--")), levels = c("--", "Underrepresented compared to low killing group",
"Overrepresented compared to low killing group"))
fold_changes.ud3.lh[is.na(fold_changes.ud3.lh)] <- "--"
sbs.ud3.low <- PlotStars(fsom_untreated, title = "Low killing donors",
nodeSizes = C_stats.ud3.lh["medians Low-killing", ],
refNodeSize = max(C_stats.ud3.lh[c("medians Low-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.lh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
sbs.ud3.high <- PlotStars(fsom_untreated, title = "High killing donors",
nodeSizes = C_stats.ud3.lh["medians High-killing", ],
refNodeSize = max(C_stats.ud3.lh[c("medians Low-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.lh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
untreateddirect3.lh <- ggpubr::ggarrange(plotlist = list(sbs.ud3.low$tree, sbs.ud3.high$tree,
sbs.ud3.high$starLegend, sbs.ud3.high$backgroundLegend),
ncol = 2, nrow = 2,
heights = c(4, 1))
# Moderate-high comparison
groups.ud3.m.h <- list("Moderate-killing" = paste0(dir_u_prep, files_untreated[c(1:4,7)]),
"High-killing" = paste0(dir_u_prep, files_untreated[c(8,9)]))
MC_stats.ud3.mh <- GroupStats(percentages[["metacluster_percentages"]], groups.ud3.m.h)
C_stats.ud3.mh <- GroupStats(percentages[["cluster_percentages"]], groups.ud3.m.h)
fold_changes.ud3.mh <- C_stats.ud3.mh["fold changes", ]
fold_changes.ud3.mh <- factor(ifelse(fold_changes.ud3.mh < -1, "Underrepresented compared to moderate killing group",
ifelse(fold_changes.ud3.mh > 1, "Overrepresented compared to moderate killing group",
"--")), levels = c("--", "Underrepresented compared to moderate killing group",
"Overrepresented compared to moderate killing group"))
fold_changes.ud3.mh[is.na(fold_changes.ud3.mh)] <- "--"
sbs.ud3.mod <- PlotStars(fsom_untreated, title = "Moderate killing donors",
nodeSizes = C_stats.ud3.mh["medians Moderate-killing", ],
refNodeSize = max(C_stats.ud3.mh[c("medians Moderate-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.mh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
sbs.ud3.high <- PlotStars(fsom_untreated, title = "High killing donors",
nodeSizes = C_stats.ud3.mh["medians High-killing", ],
refNodeSize = max(C_stats.ud3.mh[c("medians Moderate-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.mh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
untreateddirect3.mh <- ggpubr::ggarrange(plotlist = list(sbs.ud3.mod$tree, sbs.ud3.high$tree,
sbs.ud3.high$starLegend, sbs.ud3.high$backgroundLegend),
ncol = 2, nrow = 2,
heights = c(4, 1))
# Print all 3 comparisons per condition
pdf("C:/Users/Me/OneDrive - University of Nebraska at Omaha/Administrative/Documents/FUSE 2023/PhenoData/Untreated/results/untreated_ADCC3_tree.pdf")
untreateddirect3.lm
untreateddirect3.lh
untreateddirect3.mh
dev.off()
# Untreated-paired killing comparisons
percentages <-GetFeatures(fsom = fsom_untreated,
files = paste0(dir_u_prep, files_untreated),
type = "percentages")
# Low-moderate comparison
groups.ud3.l.m <- list("Low-killing" = paste0(dir_u_prep, files_untreated[c(5,6)]),
"Moderate-killing" = paste0(dir_u_prep, files_untreated[c(2:4,7)]))
MC_stats.ud3.lm <- GroupStats(percentages[["metacluster_percentages"]], groups.ud3.l.m)
C_stats.ud3.lm <- GroupStats(percentages[["cluster_percentages"]], groups.ud3.l.m)
fold_changes.ud3.lm <- C_stats.ud3.lm["fold changes", ]
fold_changes.ud3.lm <- factor(ifelse(fold_changes.ud3.lm < -1, "Underrepresented compared to low killing group",
ifelse(fold_changes.ud3.lm > 1, "Overrepresented compared to low killing group",
"--")), levels = c("--", "Underrepresented compared to low killing group",
"Overrepresented compared to low killing group"))
fold_changes.ud3.lm[is.na(fold_changes.ud3.lm)] <- "--"
sbs.ud3.low <- PlotStars(fsom_untreated, title = "Low killing donors",
nodeSizes = C_stats.ud3.lm["medians Low-killing", ],
refNodeSize = max(C_stats.ud3.lm[c("medians Low-killing", "medians Moderate-killing"),]),
backgroundValues = fold_changes.ud3.lm,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
sbs.ud3.mod <- PlotStars(fsom_untreated, title = "Moderate killing donors",
nodeSizes = C_stats.ud3.lm["medians Moderate-killing", ],
refNodeSize = max(C_stats.ud3.lm[c("medians Low-killing", "medians Moderate-killing"),]),
backgroundValues = fold_changes.ud3.lm,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
untreateddirect3.lm <- ggpubr::ggarrange(plotlist = list(sbs.ud3.low$tree, sbs.ud3.mod$tree,
sbs.ud3.mod$starLegend, sbs.ud3.mod$backgroundLegend),
ncol = 2, nrow = 2,
heights = c(4, 1))
# Low-high comparison
groups.ud3.l.h <- list("Low-killing" = paste0(dir_u_prep, files_untreated[c(5,6)]),
"High-killing" = paste0(dir_u_prep, files_untreated[c(8,9)]))
MC_stats.ud3.lh <- GroupStats(percentages[["metacluster_percentages"]], groups.ud3.l.h)
C_stats.ud3.lh <- GroupStats(percentages[["cluster_percentages"]], groups.ud3.l.h)
fold_changes.ud3.lh <- C_stats.ud3.lh["fold changes", ]
fold_changes.ud3.lh <- factor(ifelse(fold_changes.ud3.lh < -1, "Underrepresented compared to low killing group",
ifelse(fold_changes.ud3.lh > 1, "Overrepresented compared to low killing group",
"--")), levels = c("--", "Underrepresented compared to low killing group",
"Overrepresented compared to low killing group"))
fold_changes.ud3.lh[is.na(fold_changes.ud3.lh)] <- "--"
sbs.ud3.low <- PlotStars(fsom_untreated, title = "Low killing donors",
nodeSizes = C_stats.ud3.lh["medians Low-killing", ],
refNodeSize = max(C_stats.ud3.lh[c("medians Low-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.lh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
sbs.ud3.high <- PlotStars(fsom_untreated, title = "High killing donors",
nodeSizes = C_stats.ud3.lh["medians High-killing", ],
refNodeSize = max(C_stats.ud3.lh[c("medians Low-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.lh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
untreateddirect3.lh <- ggpubr::ggarrange(plotlist = list(sbs.ud3.low$tree, sbs.ud3.high$tree,
sbs.ud3.high$starLegend, sbs.ud3.high$backgroundLegend),
ncol = 2, nrow = 2,
heights = c(4, 1))
# Moderate-high comparison
groups.ud3.m.h <- list("Moderate-killing" = paste0(dir_u_prep, files_untreated[c(2:4,7)]),
"High-killing" = paste0(dir_u_prep, files_untreated[c(8,9)]))
MC_stats.ud3.mh <- GroupStats(percentages[["metacluster_percentages"]], groups.ud3.m.h)
C_stats.ud3.mh <- GroupStats(percentages[["cluster_percentages"]], groups.ud3.m.h)
fold_changes.ud3.mh <- C_stats.ud3.mh["fold changes", ]
fold_changes.ud3.mh <- factor(ifelse(fold_changes.ud3.mh < -1, "Underrepresented compared to moderate killing group",
ifelse(fold_changes.ud3.mh > 1, "Overrepresented compared to moderate killing group",
"--")), levels = c("--", "Underrepresented compared to moderate killing group",
"Overrepresented compared to moderate killing group"))
fold_changes.ud3.mh[is.na(fold_changes.ud3.mh)] <- "--"
sbs.ud3.mod <- PlotStars(fsom_untreated, title = "Moderate killing donors",
nodeSizes = C_stats.ud3.mh["medians Moderate-killing", ],
refNodeSize = max(C_stats.ud3.mh[c("medians Moderate-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.mh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
sbs.ud3.high <- PlotStars(fsom_untreated, title = "High killing donors",
nodeSizes = C_stats.ud3.mh["medians High-killing", ],
refNodeSize = max(C_stats.ud3.mh[c("medians Moderate-killing", "medians High-killing"),]),
backgroundValues = fold_changes.ud3.mh,
backgroundColors = c("white", "red", "blue"),
list_insteadof_ggarrange = TRUE)
untreateddirect3.mh <- ggpubr::ggarrange(plotlist = list(sbs.ud3.mod$tree, sbs.ud3.high$tree,
sbs.ud3.high$starLegend, sbs.ud3.high$backgroundLegend),
ncol = 2, nrow = 2,
heights = c(4, 1))
# Print all 3 comparisons per condition
pdf("C:/Users/Me/OneDrive - University of Nebraska at Omaha/Administrative/Documents/FUSE 2023/PhenoData/Untreated/results/untreated_paired3_tree.pdf")
untreateddirect3.lm
untreateddirect3.lh
untreateddirect3.mh
dev.off()