diff --git a/stress_check_all_classes.R b/stress_check_all_classes.R new file mode 100644 index 0000000..fbf963d --- /dev/null +++ b/stress_check_all_classes.R @@ -0,0 +1,68 @@ +library(Seurat) +library(SeuratDisk) +lydia <- LoadH5Seurat('F://lydia.h5Seurat0.h5seurat') +head(lydia) + + +library(ggplot2) +library(ggpubr) +library(escape) +library(patchwork) + +gene.sets1 <- getGeneSets(library = "C5", gene.sets = c('GOBP_NEURON_DEATH','GOBP_RESPONSE_TO_AXON_INJURY', + 'GOBP_INFLAMMATORY_RESPONSE', 'GOBP_INFLAMMASOME_COMPLEX_ASSEMBLY', + 'GOBP_ACUTE_INFLAMMATORY_RESPONSE', 'GOBP_CYTOKINE_PRODUCTION_INVOLVED_IN_INFLAMMATORY_RESPONSE', + 'GOBP_NEUROINFLAMMATORY_RESPONSE'), + species = 'Mus musculus') + +ES <- enrichIt(obj = lydia, + gene.sets = gene.sets1, + groups = 1000) + +lydia <- AddMetaData(lydia, ES) + +ES2 <- data.frame(lydia[[]], Idents(lydia)) +colnames(ES2)[ncol(ES2)] <- "cluster" + +lyd_RGC <- ES2 +fun_range <- function(x) { # Create user-defined function + (x - min(x)) / (max(x) - min(x))} + +neude <- aggregate(lyd_RGC$GOBP_NEURON_DEATH, list(lyd_RGC$anno2, lyd_RGC$background), FUN = mean) +neude$neude <- fun_range(x = neude$x) +resax <- aggregate(lyd_RGC$GOBP_RESPONSE_TO_AXON_INJURY, list(lyd_RGC$anno2, lyd_RGC$background), FUN = mean) +resax$resax <- fun_range(x = resax$x) + +acinf <- aggregate(lyd_RGC$GOBP_ACUTE_INFLAMMATORY_RESPONSE, list(lyd_RGC$anno2, lyd_RGC$background), FUN = mean) +acinf$acinf <- fun_range(x = acinf$x) +cytpr <- aggregate(lyd_RGC$GOBP_CYTOKINE_PRODUCTION_INVOLVED_IN_INFLAMMATORY_RESPONSE, list(lyd_RGC$anno2, lyd_RGC$background), FUN = mean) +cytpr$cytpr <- fun_range(x = cytpr$x) +infco <- aggregate(lyd_RGC$GOBP_INFLAMMASOME_COMPLEX_ASSEMBLY, list(lyd_RGC$anno2, lyd_RGC$background), FUN = mean) +infco$infco <- fun_range(x = infco$x) +infre <- aggregate(lyd_RGC$GOBP_INFLAMMATORY_RESPONSE, list(lyd_RGC$anno2, lyd_RGC$background), FUN = mean) +infre$infre <- fun_range(x = infre$x) +neure <- aggregate(lyd_RGC$GOBP_NEUROINFLAMMATORY_RESPONSE, list(lyd_RGC$anno2, lyd_RGC$background), FUN = mean) +neure$neure <- fun_range(x = neure$x) + +final <- neude +final$neude <- neude$neude +final$resax <- resax$resax +final$acinf <- acinf$acinf +final$cytpr <- cytpr$cytpr +final$infco <- infco$infco +final$infre <- infre$infre +final$neure <- neure$neure + +head(final) +final$injury <- final$resax + final$neude +final$inflam <- final$acinf + final$cytpr + final$infco + final$infre + final$neure + +final$injury_new <- fun_range(x = final$injury) +final$inflam_new <- fun_range(x = final$inflam) + +testnew <- final %>% select(Group.1, injury_new, inflam_new, Group.2) %>% + pivot_longer(., cols = c(injury_new, inflam_new), names_to = "Var", values_to = "Val") + +head(testnew) +ggplot(testnew, aes(x = reorder(Group.1, +Val), y = Val, fill = Group.2, color = Group.2, group = Group.2)) + + geom_point() + geom_line() + theme_bw() + coord_flip() + facet_wrap(~Var)