diff --git a/final_overview b/final_overview index 3214d9c0ade632071a17c1765205452929a8c50f..942c355bde1115133e91375f6a6fc279d36615fb 160000 --- a/final_overview +++ b/final_overview @@ -1 +1 @@ -Subproject commit 3214d9c0ade632071a17c1765205452929a8c50f +Subproject commit 942c355bde1115133e91375f6a6fc279d36615fb diff --git a/scripts/factor_analysis/efa_script_claire.r b/scripts/factor_analysis/efa_script_claire.r new file mode 100644 index 0000000000000000000000000000000000000000..6bc21e92925771d2aed9c3a443bbfbe1f295c1cf --- /dev/null +++ b/scripts/factor_analysis/efa_script_claire.r @@ -0,0 +1,39 @@ + + +library(lme4) # for lmer +library(memisc) # for mtable-lme4.R code +library(ggplot2) # for decent plotting +library(plyr) # for collapse-and-mean functions like ddply +library(psych) +library(GPArotation) +library(paran) +library(reshape2) + +setwd('~/Dropbox/NYU/Dimensional_Psychiatry/Analysis/efa/') + + +## plot factor analysis output +melted <- melt(load_3[,1:3])# load_3 is output for a 3 factor model where you get the loadings via: fa$loadings +melted$group_class <- substr(melted$X1, 1,3) + +melted$Questionnaire <- ifelse(melted$group_class == "OCI", "OCD", ifelse(melted$group_class == "AES","Apathy", ifelse(melted$group_class == "AUD","Alcohol Misuse",ifelse(melted$group_class == "SDS","Depression",ifelse(melted$group_class == "STA","Trait Anxiety",ifelse(melted$group_class == "EAT","Eating Disorders", ifelse(melted$group_class == "BIS","Impulsivity",ifelse(melted$group_class == "LSA","Social Anxiety",ifelse(melted$group_class == "SCZ","Schizotypy",NA))))))))) + +melted$Order <- ifelse(melted$group_class == "OCI", 3, ifelse(melted$group_class == "AES",8, ifelse(melted$group_class == "AUD",4,ifelse(melted$group_class == "SDS",6,ifelse(melted$group_class == "STA",7,ifelse(melted$group_class == "EAT",1, ifelse(melted$group_class == "BIS",2,ifelse(melted$group_class == "LSA",9,ifelse(melted$group_class == "SCZ",5,NA))))))))) + +row.names(melted) = 1:627 +melted$num <- row.names(melted) +melted = melted[order(melted$X2,melted$Order),] +melted$X1 <- factor(melted$X1, levels = subset(melted$X1,melted$X2=="ML1")) +melted$Questionnaire <- factor(melted$Questionnaire, levels = c("Eating Disorders", "Impulsivity","OCD", "Alcohol Misuse", "Schizotypy","Depression","Trait Anxiety","Apathy","Social Anxiety")) + + +barplot <- ggplot(data=melted)+ geom_bar(aes(x=X1, y=value, fill=Questionnaire, color="black"), stat="identity", binwidth=0, width=1.3)+facet_wrap(~X2, ncol=1) +theme(axis.ticks.x=element_blank(),legend.text = element_text(size = 16), strip.text = element_blank(),strip.background = element_rect(fill="white"), legend.title = element_text(size = 16, face = "bold"),axis.text.x=element_blank(), axis.title.x=element_blank(),axis.title.y=element_blank(),panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.title.y = element_text(size = rel(1.8), angle = 90), +panel.background = element_rect(fill="white"))+ scale_fill_discrete(breaks=c("Eating Disorders", "Impulsivity","OCD", "Alcohol Misuse", "Schizotypy","Depression","Trait Anxiety","Apathy","Social Anxiety")) + +#change the colours. probably a better way to do this lol +cbbPalette <- c("mediumTurquoise", "deepPink","DodgerBlue","tomato", "palegoldenrod", "mediumseagreen", "DarkGoldenRod", "mediumblue","MediumOrchid") +borders <- c("gray14","gray14","gray14","gray14","gray14","gray14","gray14","gray14","gray14","gray14") +barplot+ scale_fill_manual(values=cbbPalette)+ scale_colour_manual(values=borders)+ guides(color= FALSE) + +ggsave(filename="figures/study2_efa_loadings.png") + diff --git a/scripts/very_important_file.txt b/scripts/very_important_file.txt new file mode 100644 index 0000000000000000000000000000000000000000..d6ba7144ccf66849e70d4bca1ee79de82d38e7bf --- /dev/null +++ b/scripts/very_important_file.txt @@ -0,0 +1 @@ +Very!