adjusting the legend in TramineR plots

Question

I am new to using TramineR and I just cannot seem to figure out how to arrange the legend in any of the plot types. The legend keeps being cut off by the plots. I have tried to use the seqlegend command but I do not understand how I would integrate the separate legend into my plots.

dat <- data.frame(matrix(sample(0:13, 300 * 26, replace = TRUE), ncol = 26))
dat$age50 <- sample(c("yes", "no"), 300, replace = TRUE)

# Create state sequence object
cci.seq <- seqdef(dat, 
                  var = 1:26, 
                  alphabet = c("0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "99"))

# Recode the sequence object
cci.new <- seqrecode(cci.seq, 
                     recodes = list("0 CCI" = "0", 
                                    "1-2 CCI" = c("1", "2"), 
                                    "3-4 CCI" = c("3", "4"), 
                                    "5-6 CCI" = c("5", "6"),
                                    "7-8 CCI" = c("7", "8"), 
                                    "10+ CCI" = c("9", "10", "11", "12", "13"), 
                                    "death" = c("99")))

# Define color palette
cpal(cci.new) <- c("#CAE1EE", "#0772b4", "#f2c673", "#df3337", "#f29862", "#2fa791", "#8A2BE2")

# Basic plot
seqIplot(cci.new, 
         with.legend = TRUE,
         bty = "n",
         idxs = 1:300,
         group = dat$age50,
         legend.prop = 0.1,
ncol=2,
         main = "300 individual sequences by disability status")

I have tried adjusting the cex.legend but it makes the text too small to read.

Answer 1

If there is not enough space on the canvas for your legend, you could consider changing the size of your plot by calling dev.new(). For example, by typing

dev.new(width = 14, height = 8, unit="in")

Note that you have to add noRStudioGD = TRUE if you are working in RStudio.

If you want to save your plot and not just look at it in an interactive R session, you could test different size specifications until you find one that fits the legend. I personally prefer saving base R plots as pdf (and convert them to png with pdftools::pdf_convert() if necessary):

pdf("iplot.pdf",
    width = 14, height = 8)

seqIplot(cci.new, 
         with.legend = TRUE,
         bty = "n",
         group = dat$age50,
         legend.prop = 0.1,
         ncol=4,
         main = "300 individual sequences by disability status")

dev.off()

Alternatively, you could change to {ggplot2} plot environment using the package {ggseqplot}.

library(ggseqplot)

ggseqiplot(cci.new, 
           group = dat$age50) +
  labs(title = "300 individual sequences by disability status")

Answer 2

Several arguments of the seqplot family functions of TraMineR such as cex.legend, legend.prop can be used to control the legend. In addition, most arguments of legend such as ncol can be passed among the ... argument list.

I illustrate with the actcal data:

data(actcal)
## We use only a sample of 300 cases
set.seed(1)
actcal <- actcal[sample(nrow(actcal),300),]
actcal.lab <- c("> 37 hours", "19-36 hours", "1-18 hours", "no work")
actcal.seq <- seqdef(actcal,13:24,labels=actcal.lab)

seqdplot(actcal.seq, group=actcal$sex, ncol=4, legend.prop=.1, cex.legend=1.2)

---

Edit

For the example you have added in your question, you should increase the proportion of the plot (legend.prop) left for the legend. For example, the following seems to work fine:

seqIplot(cci.new, 
         with.legend = TRUE,
         bty = "n",
         idxs = 1:300,
         group = dat$age50,
         legend.prop = 0.2,
         cex.legend=1.2,
         ncol=4,
         main = "300 individual sequences by disability status")