Collection of scripts for analyses and plots we usually make in the lab.

Table of Contents

Stats: Linear mixed effects models

# LINEAR MIXED EFFECTS MODELS
# For linear mixed effects models on "Open Field Data" use lmer, and then use anova to find the F and p-values. The creators of lmer are opposed to p-values for lmer does not automatically give it.

Mixopenfield = lmer(value ~ Condition * variable + (1|Mouse), 
                    data=arishopenfield,
                    REML = FALSE)
anova(Mixopenfield)

# PAIRWISE COMPARISONS USING EMMEANS
emmeans(Mixopenfield, list(pairwise ~ variable*Condition), adjust = "tukey")

Graph: Bar with points

#These will give bar graphs with a dot representing each data point overlayed on the bar.

BarOpenField = ggplot(data=arishopenfield, aes(x=Condition, y=value, fill=variable)) +
  geom_bar(stat="summary", fun.y="mean", position=position_dodge()) + 
  labs(#title = "Open Field Data",
    #       caption = "WRITE A CAPTION",
    #       tag = "Figure #",
    x = "Housing Condition",
    y = "Time spent in center of field (seconds)") +
  geom_dotplot(aes(fill = variable, color = variable), trim = FALSE,
               binaxis='y', stackdir='center', dotsize = 0.8,
               position = position_dodge(), show.legend = FALSE ) +
  theme_bw() +
  scale_fill_manual(name="Stress Exposure", 
                    labels = c("Pre-Stress","Post-Stress"),
                    values=c('dark grey','light grey')) +
  scale_color_manual(values = c("black", "black"))
ggsave("OpenField.tif", plot = BarOpenField, dpi = 300, device = "tiff")