Is it possible to subset facets in a polyfreq in GGplot?

Question

I was wondering if it was possible to use subset on a geom_polyfreq()?

I am running a topic model and in order to report the facets properly i want to remove 4 out of 10 facets.

My code is as follows:

  ggplot(data = dat,
                 aes(x = date,
                     fill = Topics)) +
            geom_freqpoly(binwidth = 3) +
        labs(x = "", 
               y = "Topic Count",
               title = "Mentions of Topic On a Monthly Basis")+
        scale_x_date(date_breaks = "months", date_labels="%b")+
        theme(text = element_text(size=8)) +
        theme(axis.text.x = element_text(angle = 45))+
        facet_wrap(Topics ~ ., scales = "free")


> ggplot(subset(dat, Topics %in% c(3, 4, 5, 7, 8, 9)),
          aes(x = date,
              fill = topic)) +
     geom_freqpoly(binwidth = 3) +
 labs(x = "", 
        y = "Topic Count",
        title = "Mentions of Topic On a Monthly Basis")+
scale_x_date(date_breaks = "months", date_labels="%b")+
theme(text = element_text(size=9)) +
theme(axis.text.x = element_text(angle = 45))+
facet_wrap(Topics ~ ., scales = "free")

However, when I try to subset the data, I get an error that says: Fejl: Faceting variables must have at least one value

Does anybody know what the issue is? I hope this makes sense.

The full code is down below.

article.data <- article.data[!is.na(article.data$fulltext), ]

## Get date
article.data$date <- as.Date(article.data$date, "%Y-%m-%d")

#all of 2018
dat <- article.data[article.data$date > as.Date("2018-01-01", "%Y-%m-%d") & 
                       article.data$date < as.Date("2018-12-01", "%Y-%m-%d"), ]


## 'tokenize' fulltext
quanteda_options("language_stemmer" = "danish")
texts <- gsub(":", " ", dat$fulltext, fixed = T)

texts <- tokens(texts, what = "word",
                remove_numbers = T,
                remove_punct = T,
                remove_symbols = T,
                remove_separators = T,
                remove_hyphens = T,
                remove_url = T,
                verbose = T)

texts <- tokens_tolower(texts)
texts <- tokens_remove(texts, stopwords("danish"))
texts <- tokens_wordstem(texts)
texts <- tokens_remove(texts, stopwords("danish"))

# get actual dfm from tokens
txt.mat <- dfm(texts)

#remove frequent words with no substance
txt.mat <- txt.mat %>% dfm_remove(c("ad",
                                    "af","aldrig","alene","alle",
                                    "allerede","alligevel","alt",
                                    "altid","anden","andet","andre",
                                    "at","bag","bare", "bedre", "begge","bl.a.",
                                    "blandt", "blev", "blevet", "blive","bliver",
                                    "burde", "bør","ca.", "com", "da", 
                                    "dag", "dansk", "danske", "de",
                                    "dem", "den", "denne","dens",
                                    "der","derefter","deres","derfor",
                                    "derfra","deri","dermed","derpå",
                                    "derved","det","dette","dig",
                                    "din","dine","disse","dit",
                                    "dog","du","efter","egen",
                                    "ej","eller","ellers","en",
                                    "end","endnu","ene","eneste","enhver","ens",
                                    "enten","er","et","f.eks.","far","fem",
                                    "fik","fire","flere","flest",
                                    "fleste","for", "foran",
                                    "fordi","forrige","fra", "fx",
                                    "få","får","før","først",
                                    "gennem","gjorde","gjort","god",
                                    "godt","gør","gøre","gørende",
                                    "ham","han","hans","har",
                                    "havde","have","hej","hel",
                                    "heller","helt","hen","hende",
                                    "hendes","henover","her",
                                    "herefter","heri","hermed",
                                    "herpå","hos","hun","hvad",
                                    "hvem","hver","hvilke","hvilken",
                                    "hvilkes","hvis",
                                    "hvor", "hvordan","hvorefter","hvorfor",
                                    "hvorfra","hvorhen","hvori","hvorimod",
                                    "hvornår","hvorved","i", "ifølge", "igen",
                                    "igennem","ikke","imellem","imens",
                                    "imod","ind","indtil","ingen",
                                    "intet","ja","jeg","jer","jeres",
                                    "jo","kan","kom","komme",
                                    "kommer", "kroner", "kun","kunne","lad",
                                    "langs", "lang", "langt", "lav","lave","lavet",
                                    "lidt","lige","ligesom","lille",
                                    "længere","man","mand","mange",
                                    "med","meget","mellem","men", "mener",
                                    "mens","mere","mest","mig",
                                    "min","mindre","mindst","mine",
                                    "mit","mod","må","måske",
                                    "ned","nej","nemlig","ni",
                                    "nogen","nogensinde","noget",
                                    "nogle","nok","nu","ny", "nye",
                                    "nyt","når","nær","næste",
                                    "næsten","og","også","okay",
                                    "om","omkring","op","os",
                                    "otte","over","overalt","pga.", "partier",
                                    "partiets", "partiers", "politiske",
                                    "procent", "på", "ritzau", "samme", 
                                    "sammen","se","seks","selv","selvom",
                                    "senere","ser","ses","siden","sig",
                                    "sige", "siger", "sin","sine","sit",
                                    "skal","skulle","som","stadig",
                                    "stor","store","synes","syntes",
                                    "syv","så","sådan","således",
                                    "tag","tage","temmelig","thi",
                                    "ti","tidligere","til","tilbage",
                                    "tit","to","tre","ud","uden",
                                    "udover","under","undtagen","var",
                                    "ved","vi","via","vil","ville", "viser", 
                                    "vor","vore","vores","vær","være",
                                    "været","øvrigt","facebook","http", "https",
                                    "www","millioner", "frem", "lars", "lars_løkke", 
                                    "rasmussen", "løkke_rasmussen", "statsminister", "politik",
                                    "formand", "partiet", "år", "tid", "and", "fler",
                                    "sid", "regeringen", "giv", "politisk", "folketing", "mer",
                                    "ifølg"))

############################################################
## FEATURE SELECTION
############################################################

# check out top-appearing features in dfm
topfeatures(txt.mat)

# keep features (words) appearing in >2 documents
txt.mat <- dfm_trim(txt.mat, min_termfreq = 4)

# filter out one-character words
txt.mat <- txt.mat[, str_length(colnames(txt.mat)) > 2]

# filter out some html trash features
#txt.mat <- txt.mat[, !grepl("[[:digit:]]+px", colnames(txt.mat))]
#txt.mat <- txt.mat[, !grepl(".", colnames(txt.mat), fixed = T)]
#txt.mat <- txt.mat[, !grepl("_", colnames(txt.mat), fixed = T)]
#txt.mat <- txt.mat[, !grepl("@", colnames(txt.mat), fixed = T)]
#txt.mat <- txt.mat[, !grepl("#", colnames(txt.mat), fixed = T)]


############################################################
## SELECT FEATURES BY TF-IDF
############################################################

# Create tf_idf-weighted dfm
ti <- dfm_tfidf(txt.mat)

# Select from main dfm using its top features
txt.mat <- dfm_keep(txt.mat, names(topfeatures(ti, n = 1000)))


############################################################
## RUN TOPIC MODEL
############################################################

# convert quanteda dfm to tm 'dtm'
dtm <- convert(txt.mat, to = "topicmodels")

# run lda with 8 topics
lda <- LDA(dtm, k = 8)

# review terms by topic
terms(lda, 10)


############################################################
## LOOK FOR 'OPTIMAL' k
############################################################

# randomly sample test data
set.seed(61218)
select <- sample(1:nrow(dtm), size = 100)
test <- dtm[select, ]
train <- dtm[!(1:nrow(dtm) %in% select), ]

n.tops <- 3:14
metrics <- data.frame(topics = n.tops,
                      perplexity = NA)

for(i in n.tops) { # NB: takes awhile to run
  print(i)
  est <- LDA(train, k = i)
  metrics[(i - 1), "perplexity"] <- perplexity(est, newdata = test)
}

save(metrics, file = "lda_perplexity2018.RData")

qplot(data = metrics, x = topics, y = perplexity, geom = "line",
      xlab = "Number of topics",
      ylab = "Perplexity on test data") + theme_bw()

#We found that 8 topics was one of those of lowest perplexity but 
#also the ones which made the most sense

############################################################
## RERUN WITH BETTER CHOICE OF k
############################################################

# run lda with 10 topics
lda <- LDA(dtm, k = 10)
save(lda, file = "dr_ft_keep2018.RData")

# examine output
terms(lda, 20)

# put topics into original data
dat$topic <- topics(lda)


# add labels
#dat$date <- factor(dat$date,
#levels = 1:12,
#labels = c("januar","februar", "marts","april", "maj", "juni", "juli", "august", "september", "oktober", "november", "decemeber"))

dat$Topics <- factor(dat$topic,
                     levels = 1:10,
                     labels = c("Topc 1", "Topic 2", "Integration", "Taxation", "Burka Prohibition", 
                                "Topic 6", "Justice", "Foreign Affairs", "Housing", "Topic 10"))


# frequency
qplot(data = dat, x = Topics, 
      geom = "bar", xlab = "", 
      ylab = "Topic Frequency", fill=Topics, main = "Figure 1: Main Topics in 2018 - DR") + 
  theme_bw() +
  theme(axis.text.x = element_text(angle = 90))


#Make visualization showing topics over time
ggplot(data = dat,
       aes(x = date,
           fill = Topics[1])) +
  geom_freqpoly(binwidth = 30) +
  facet_wrap(Topics ~ ., scales = "free")+
theme_classic() +
scale_x_date(breaks = as.Date(c( "2018-02-01", "2018-04-01",  "2018-06-01",  "2018-08-01",  "2018-10-01", "2018-12-01",  date_labels="%B"))) + 
theme(axis.text.x = element_text(angle = 90)) 


ggplot(data = dat,
         aes(x = date,
             fill = Topics)) +
    geom_freqpoly(binwidth = 3) +
labs(x = "", 
       y = "Topic Count",
       title = "Mentions of Topic On a Monthly Basis")+
scale_x_date(date_breaks = "months", date_labels="%b")+
theme(text = element_text(size=8)) +
theme(axis.text.x = element_text(angle = 45))+
facet_wrap(Topics ~ ., scales = "free")

Answer 1

It's best practice on this forum to make your question reproducible, so that others can try it and test their solutions to confirm they work. It's also good if you can make it minimal, both to respect potential answerers' time and to help clarify your own understanding of the problem.

How to make a great R reproducible example

In this case, the error message suggests that your subsetting is removing all your data, which breaks the faceting. It can't plot any facets if the faceting variable has no values.

It looks like dat$Topics is a factor, but your loop is referring to Topics like they're numeric with Topics %in% c(3, 4, 5, 7, 8, 9). For example, I could define a factor vector with the same levels as your Topics variable:

Topics <- factor(1:10, levels = 1:10,
                 labels = c("Topc 1", "Topic 2", "Integration", "Taxation", "Burka Prohibition", 
                                "Topic 6", "Justice", "Foreign Affairs", "Housing", "Topic 10"))

Compare the output of these three lines:

Topics %in% c(1, 2)
# [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
as.numeric(Topics) %in% c(1, 2)
# [1]  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
Topics %in% c("Topc 1", "Topic 2")
# [1]  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE

In the top case, none of the data matches the test, so using that to subset the data would give you an empty data set and seems like a plausible cause for the error you got.

To refer to the Topics by their underlying level, we can refer to as.numeric(Topics) %in% c(1, 2). If we want to refer to the Topics by their labels, I could use Topics %in% c("Topc 1", "Topic 2").

Since I don't have your data, I can't confirm this exact syntax will work for you, but I hope something along these lines will.

For more on how to work with factors in R, I recommend: https://r4ds.had.co.nz/factors.html