Visualizing Categorizations blog post code

visualizing-categorizations.R

# Demo of techniques to visualize the predictions made by a categorization model.

library(ROCR)
library(ggplot2)

load(url('http://dl.dropbox.com/u/7644953/classifier-visualization.Rdata'))

pred.df$actual.bin <- ifelse(pred.df$actual == 'yes', 1, 0)
pred.df <- pred.df[order(pred.df$predicted, decreasing=TRUE), ]

pred.df$cumsum <- cumsum(pred.df$actual.bin)/sum(pred.df$actual.bin)
pred.df$cumsum.yes <- with(pred.df, cumsum * actual.bin)

head(pred.df)
summary(pred.df)

baserate <- mean(pred.df$actual.bin)

# visualizations using ROCR

# convert to their object type (labels should be some sort of ordered type)
pred.rocr <- prediction(pred.df$predicted, pred.df$actual)

# some scalar summary stats
# Area Under the ROC Curve
performance(pred.rocr, 'auc')@y.values[[1]]
# Precision/Recall breakeven
performance(pred.rocr, 'prbe')@x.values[[1]]

# some ROCR graphs
# ROC Curve
plot(performance(pred.rocr, 'tpr', 'fpr'))
# Sensitivity/Specificity
plot(performance(pred.rocr, 'sens', 'spec'))
# Lift Curve
plot(performance(pred.rocr, 'lift', 'rpp'))

lift.perf <- performance(pred.rocr, 'lift', 'rpp')
lift.df <- data.frame(predicted=lift.perf@alpha.values[[1]], # alpha is cutoff
    lift=lift.perf@y.values[[1]])
lift.df <- lift.df[2:nrow(lift.df), ]

# decile table
dec.table <- ldply((1:10)/10, function(x) data.frame(
    decile=x,
    prop.yes=sum(pred.df$actual.bin[1:ceiling(nrow(pred.df)*x)])/sum(pred.df$actual.bin),
    lift=mean(pred.df$actual.bin[1:ceiling(nrow(pred.df)*x)])/mean(pred.df$actual.bin)))
print(dec.table, digits=2)

# dual smear graph
plot.dual.smear <- ggplot(pred.df, aes(predicted, actual.bin)) + 
  geom_jitter(alpha=.3, position=position_jitter(height=.04,width=0)) + 
  stat_smooth() +
  geom_abline(slope=1, intercept=0, color='grey', size=.1) + 
  geom_vline(xintercept=baserate, color='orange', size=.5) +
  scale_x_continuous('Predicted', breaks=(0:4)/4, limits=c(0,.75), labels=sprintf('%d%%', (0:4)*25)) +
  scale_y_continuous('Actual', breaks=(0:4)/4, limits=c(-.05,1.05), labels=c('No', '', '', '', 'Yes')) +
  coord_equal()

# single smear graph
plot.single.smear <- ggplot(pred.df, aes(predicted, actual.bin, colour=actual)) +
  geom_jitter(alpha=.3, position=position_jitter(height=.5,width=0)) +
  geom_line(data=lift.df, aes(y=lift, color=NULL)) +
  scale_color_manual(values=c('darkblue', 'darkred')) +
  scale_x_continuous('Predicted', breaks=(0:4)/4, limits=c(0,.75), labels=sprintf('%d%%', (0:4)*25)) +
  scale_y_continuous('Lift') +
  geom_vline(xintercept=baserate, color='orange', size=.5) +
  geom_hline(yintercept=1, color='darkgrey', size=.5)
  
# dual smear with cumulative reach of yesses
plot.dual.cumulative <- ggplot(pred.df, aes(predicted, cumsum.yes, colour=actual)) + 
  geom_jitter(alpha=.3, position=position_jitter(height=.04,width=0)) + 
  geom_vline(xintercept=baserate, color='orange', size=.5) +
  scale_color_manual(values=c('darkblue', 'darkred')) +
  scale_x_continuous('Predicted/Threshold', breaks=(0:4)/4, limits=c(0,.75), labels=sprintf('%d%%', (0:4)*25)) +
  scale_y_continuous('Cumulative Proportion of Yesses Seen') 

# pos/neg densities
plot.densities <- ggplot(pred.df, aes(predicted, ..count.., fill=actual)) + 
  stat_density(alpha=.5, position='identity') +
  scale_x_continuous('Predicted', breaks=(0:4)/4, limits=c(0,1), labels=sprintf('%d%%', (0:4)*25)) +
  scale_y_sqrt('Density')
  
  
  

It it OK to use 4 lines of this (78 to 82) for my research (Master's Thesis)?

Aleksandr, sure! It's in the public domain. If you feel like citing me, a footnote (not a formal citation) with my name and a link to the gist would be appreciated. What's your topic? (Email me directly -- my email address is easy to google.)

Harlan, Thanks! Couldn't find your email but added you to my Google+. I'm doing Bioinformatics research. The topic is: Removing Badly Aligned or Unrelated Sequences from Multiple Sequence Alignments. So, here is one of the places where you're code ends up: alevchuk/ms@f348713#L0R37