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ggplot2_coefplot
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| # Load libraries | |
| lapply(c("datasets","arm","ggplot2","RColorBrewer","grid"),library, character.only=TRUE) | |
| # Set working directory and load data | |
| setwd("~/R") | |
| data(mtcars) | |
| # Fit a linear model of mpg ~ wt + disp + hp + qsec | |
| fit.1 <-lm(mpg ~ wt + disp + hp + qsec, data=mtcars) | |
| display(fit.1) | |
| # Rescale the model | |
| fit.2 <- standardize(fit.1) | |
| # Extract parameters | |
| coefs <- summary (fit.2)$coef[, 1] | |
| sds <- summary(fit.2)$coef[, 2] | |
| # Generate lower and upper bounds | |
| coef.min <-coefs-(1.96*sds) | |
| coef.max <-coefs+(1.96*sds) | |
| coef.sd.min <-coefs-sds | |
| coef.sd.max <-coefs+sds | |
| # Generate variable names | |
| longnames <-c("Intercept","Weight", "Displacement", "Horsepower", "Quarter-mile time") | |
| # Create data frame | |
| d <-data.frame(coefs,sds,coef.min, coef.max, coef.sd.min,coef.sd.max, longnames) | |
| # Order parameter names | |
| d$longnames.1 <- as.character(d$longnames) | |
| d$longnames <- factor(d$longnames.1, levels=rev(unique(d$longnames.1))) | |
| # Generate relevant shades | |
| palette <- brewer.pal("Greys", n=9) | |
| color.background = palette[2] | |
| color.grid.major = palette[3] | |
| color.axis.text = palette[6] | |
| color.axis.title = palette[7] | |
| color.title = palette[9] | |
| # Plot | |
| k <-ggplot() + | |
| geom_pointrange(data=d, mapping=aes(x=d$longnames,y=d$coefs, ymin=d$coef.min, ymax=d$coef.max), position="identity", width=0.25, size=0.5, color="black") + | |
| geom_pointrange(data=d, mapping=aes(x=d$longnames,y=d$coefs, ymin=d$coef.sd.min, ymax=d$coef.sd.max), position="identity", width=0.5, size=1, color="black") + | |
| theme_bw() + | |
| # Set the entire chart region to a light gray color | |
| theme(panel.background=element_rect(fill=color.background, color=color.background)) + | |
| theme(plot.background=element_rect(fill=color.background, color=color.background)) + | |
| theme(panel.border=element_blank(), axis.line=element_line(), axis.line.y=element_blank()) + | |
| # Format the grid | |
| theme(panel.grid.major=element_line(colour=color.background,size=.75)) + | |
| theme(axis.ticks=element_blank()) + | |
| theme(axis.line.x =element_line(colour="#535353", size=.75))+ | |
| # Dispose of the legend | |
| theme(legend.position="none") + | |
| # Set title and axis labels, and format these and tick marks | |
| ggtitle("Regression Estimates") + | |
| theme(plot.title = element_text(size = 20, hjust=-.8, vjust=2.6, face="bold"))+ | |
| xlab("") + | |
| ylab("Change in miles per gallon (US)") + | |
| theme(axis.text.x=element_text(size=11,colour="#535353",face="bold")) + | |
| theme(axis.text.y=element_text(size=11,colour="#535353",face="bold")) + | |
| theme(axis.title.y=element_text(size=11,colour="#535353",face="bold",vjust=1.5)) + | |
| theme(axis.title.x=element_text(size=11,colour="#535353",face="bold",vjust=-.5)) + | |
| # Big bold line at y=0 | |
| geom_hline(yintercept=0,size=1.2, alpha=0.2,colour="#535353", linetype="twodash")+ | |
| # Plot margins | |
| theme(plot.margin = unit(c(1, 1, .5, .7), "cm")) | |
| k + coord_flip() | |
| ggsave("coefplot_mtcars.png", dpi=150, width=7, height=3) |
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