Closed GKok closed 1 year ago
teunbrand
commented
1 year ago It is hard to know without a reproducible example, but my guess is that data isn't the only data provided to the plot and some other part might be missing some of the facetting variables.
GKok
commented
1 year ago Not sure if it's op any help, but here's a reprex-output. It shows many errors, but the Excel-file is properly loaded, despite what it shows.
library(ggplot2)
library(scales)
library(ggalt)
#> Registered S3 methods overwritten by 'ggalt':
#> method from
#> grid.draw.absoluteGrob ggplot2
#> grobHeight.absoluteGrob ggplot2
#> grobWidth.absoluteGrob ggplot2
#> grobX.absoluteGrob ggplot2
#> grobY.absoluteGrob ggplot2
library(gdata)
#> gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
#>
#> gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
#>
#> Attaching package: 'gdata'
#> The following object is masked from 'package:stats':
#>
#> nobs
#> The following object is masked from 'package:utils':
#>
#> object.size
#> The following object is masked from 'package:base':
#>
#> startsWith
library(tidyverse)
library(extrafont)
#> Registering fonts with R
library(ggpubr)
library(grDevices)
#remotes::install_github("teunbrand/ggh4x")
library(ggh4x)
library(reprex)
theme_set(theme_minimal(base_family="Myriad Pro"))
theme_update(text = element_text(family = "Myriad Pro"))
data = read.xls('Data-HLA.xlsx')
#> Warning in system(cmd, intern = !verbose): running command ''/usr/bin/perl'
#> '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/gdata/perl/
#> xls2csv.pl' 'Data-HLA.xlsx' '/var/folders/hl/ljvw4xb15_b2ff_y5ts5vpb80000gn/T//
#> RtmpRMmNqE/file3a101cb0ca3c.csv' '1'' had status 2
#> Error in xls2sep(xls, sheet, verbose = verbose, ..., method = method, : Intermediate file '/var/folders/hl/ljvw4xb15_b2ff_y5ts5vpb80000gn/T//RtmpRMmNqE/file3a101cb0ca3c.csv' missing!
#> Error in file.exists(tfn): invalid 'file' argument
#data = read.xls('Data-HLA-supplement.xlsx')
data$test <- forcats::fct_inorder(data$test)
#> Error in data$test: object of type 'closure' is not subsettable
data$HLA <- forcats::fct_inorder(data$HLA)
#> Error in data$HLA: object of type 'closure' is not subsettable
data$outcome <- forcats::fct_inorder(data$outcome)
#> Error in data$outcome: object of type 'closure' is not subsettable
data <- data %>% arrange(year, author) %>% mutate(year=forcats::fct_inorder(factor(year))) %>% arrange(-row_number())
#> Error in UseMethod("arrange"): no applicable method for 'arrange' applied to an object of class "function"
data$author_year <- forcats::fct_inorder(paste(data$author, data$year))
#> Error in data$author: object of type 'closure' is not subsettable
data$author_year <- forcats::fct_inorder(str_replace(data$author_year, " NA", ""))
#> Error in data$author_year: object of type 'closure' is not subsettable
plot_outcome <- function (dataset) {
plot <- ggplot(na.omit(dataset), aes(y=author_year, color=shape))
plot +
scale_x_log10(limits = c(0.01, 100),
breaks = scales::trans_breaks("log10", function(x) 10^x),
labels = ~ gsub("\\.?0+$", "", comma(.x))) +
geom_vline(aes(xintercept=1),
linetype="dotted") +
theme(panel.grid.major.x=element_line(size=0.5),
panel.grid.minor.x=element_blank(),
axis.title.y=element_blank(),
strip.placement = "outside",
strip.text.x = element_text(face = "bold"),
strip.text.y = element_text(face = "bold"),
strip.background = element_rect(colour = "white", fill = "gray95"),
panel.spacing.x = unit(1,"line")) +
facet_nested(outcome + test ~ HLA,
switch="y",
labeller = labeller(outcome = c("AR" = "Acute rejection",
"CR" = "Chronic rejection",
"GL1" = "Graft failure (1-year)",
"GL2" = "Graft failure (2-year)",
"GL5" = "Graft failure (5-year)",
"M1" = "Mortality (1-year)",
"M5" = "Mortality (5-year)"),
test = c("0-1" = "0 vs. 1 MM",
"0-2" = "0 vs. 2 MM",
"1-2" = "1 vs. 2 MM"),
HLA = c("A" = "HLA-A",
"B" = "HLA-B",
"C" = "HLA-C",
"DR" = "HLA-DR",
"DQ" = "HLA-DQ")),
scales = "free_y",
space = "free_y"
) +
scale_size(guide="none") +
scale_shape_manual(values = c(18,16),
guide="none") +
scale_colour_manual(values = c(2, 1),
guide="none") +
labs(x="Relative risk") +
geom_point(aes(x=RR,
size=weight,
shape=as.factor(shape)),
position = position_dodge(width=0.8)) +
geom_dumbbell(aes(x=ifelse(CI.lower < 0.01, 0.01, CI.lower),
xend=ifelse(CI.upper > 100, 100, CI.upper)),
size_x=0,
size_xend=0,
position = position_dodgev(height=-0.8)) +
geom_segment(aes(x = ifelse(CI.upper > 100, 99, NA),
xend = ifelse(CI.upper > 100, 100, NA),
yend=author_year),
arrow = arrow(length = unit(0.15, "cm"))) +
geom_text(aes(x = RR+2,
label=ifelse(is.na(P), "", paste0("RR = ", comma(RR, accuracy = 0.01), " [", comma(CI.lower, accuracy = 0.01), "-", comma(CI.upper, accuracy = 0.01), "]\nP = ", comma(P, accuracy = 0.01)))),
color="black",
position = position_dodge(width=0.8),
size=3,
hjust = 0,
fontfamily="Myriad Pro")
}
plotall <- plot_outcome(data)
#> Error in `ggplot()`:
#> ! You're passing a function as global data.
#> Have you misspelled the `data` argument in `ggplot()`
plotall
#> Error in eval(expr, envir, enclos): object 'plotall' not foundI have also attached the Excel file.
This exact script + datafile worked previously to create the attached plot.
Many thanks!
teunbrand
commented
1 year ago From executing your code, I gather that na.omit() drops every row of the dataset. So indeed, the facetting variables do not have a value. You get the same error when you use facet_grid(), so I don't think this is an issue with ggh4x.
For future reference, people diagnosing possible problems with code would think it is great if reprexes are more minimal. Now, I had to install several packages I don't use just to run the code, and weed through many lines of code that weren't relevant to the problem (I know this sounds grumpy, but it's not intended this way :D). This specific example could have been the following reprex:
library(ggplot2)
library(ggh4x)
plot_outcome <- function(dataset) {
ggplot(na.omit(dataset), aes(Sepal.Width, Sepal.Length)) +
geom_point() +
facet_nested(~ Species)
}
plot_outcome(cbind(iris, na_col = NA))
#> Error: Facetting variables must have at least one valueThank you Teun.
My apologies for the issue not being related; I missed that, presumably because the exact same code worked previously and I was too focussed on facet_nested(). And I'll take your advice and will make a more specific/short reprex.
I appreciate your work. Have a good weekend!
I'm getting a new error with a script that previously worked, presumably after updating ggh4x. I tried the development build, but that didn't solve it.
I have a dataset with various variables. I'm trying to draw a figure with the following code:
This throws the following error:
However, all facetting variables have multiple values:
Now some facets may be empty, as not all datapoints are available for every facet. That was not a problem previously, but I'm not sure now.
Any idea what's going on? Thanks a lot for your help!