stacked bar chart issues: Error in FUN(X[[i]], ...)

[rhimack]

1. i had to re-classify types of pupil abnormalities

sub$pupil_auto <- paste(sub$normalpupil, sub$pupil_abn, sep = ":")

sub$pupil_auto <- ifelse(sub$pupil_auto == "1:NA", "normal", sub$pupil_auto)
sub$pupil_auto <- ifelse(sub$pupil_auto == "2:1", "sympathetic", sub$pupil_auto)
sub$pupil_auto <- ifelse(sub$pupil_auto == "2:2", "parasympathetic", sub$pupil_auto)
sub$pupil_auto <- ifelse(sub$pupil_auto == "2:3", "both", sub$pupil_auto)
sub$pupil_auto <- ifelse(sub$pupil_auto == "1:1", "sympathetic", sub$pupil_auto)
sub$pupil_auto <- ifelse(sub$pupil_auto == "NA:NA", NA, sub$pupil_auto)

sub$pupil_auto <- as.factor(sub$pupil_auto)
class(sub$pupil_auto)

2. reorder groups in preparation for plot

sub$pupil_auto <- factor(sub$pupil_auto,
levels = c("both", "parasympathetic", "sympathetic", "normal"), ordered = TRUE)

table(sub$pupil_auto, sub$final_dx_groups2)

3. stacked bar chart coding

png("Pupil_barchart.png",width = 800, height = 480)
ecols <- c(normal="seashell", sympathetic = "pink", parasympathetic = "steelblue1", both = "orchid")
ggplot(data = subpup,aes(x = final_dx_groups2, fill = pupil_auto)) + geom_bar() +
scale_fill_manual(values = ecols) +
theme(text = element_text(size=18), axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) +
labs(fill = "Pupil deficits") +
ylab("Number of patients") +
xlab("Final Diagnosis") +
ggtitle("Pupillometry")
dev.off()

error received:
Error in FUN(X[[i]], ...) : object 'pupil_auto' not found

HELP!

[nirgrahamuk]

your chart is being made from subpup which has no other mention in your code.
It seemed like it would have been sub, as that has many mentions.

[rhimack]

I changed it to sub (thank you for noticing), this solved my error in FUN(X[[i]],...) and now my graph looks like this:

how would I bring the box plots down to the x axis?

[nirgrahamuk]

ggplot offers functions to alter the axis limits.
see : Set scale limits — lims • ggplot2 (tidyverse.org)

[rhimack]

thanks for your help