print("HI")[1] "HI"library(tidyverse)
library(readxl)
install.packages("extrafont") # Install extrafont
library(extrafont) # Load extrafont for consistent font handling
font_import(prompt = FALSE) # Import system fonts (can take a few minutes)Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘extrafontdb’, ‘Rttf2pt1’
Registering fonts with R
Scanning ttf files in /usr/share/fonts/, /usr/local/share/fonts/ ...
Extracting .afm files from .ttf files...
/usr/share/fonts/truetype/humor-sans/Humor-Sans.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/Humor-Sans
/usr/share/fonts/truetype/liberation/LiberationMono-Bold.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationMono-Bold
/usr/share/fonts/truetype/liberation/LiberationMono-BoldItalic.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationMono-BoldItalic
/usr/share/fonts/truetype/liberation/LiberationMono-Italic.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationMono-Italic
/usr/share/fonts/truetype/liberation/LiberationMono-Regular.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationMono-Regular
/usr/share/fonts/truetype/liberation/LiberationSans-Bold.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationSans-Bold
/usr/share/fonts/truetype/liberation/LiberationSans-BoldItalic.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationSans-BoldItalic
/usr/share/fonts/truetype/liberation/LiberationSans-Italic.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationSans-Italic
/usr/share/fonts/truetype/liberation/LiberationSans-Regular.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationSans-Regular
/usr/share/fonts/truetype/liberation/LiberationSerif-Bold.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationSerif-Bold
/usr/share/fonts/truetype/liberation/LiberationSerif-BoldItalic.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationSerif-BoldItalic
/usr/share/fonts/truetype/liberation/LiberationSerif-Italic.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationSerif-Italic
/usr/share/fonts/truetype/liberation/LiberationSerif-Regular.ttf
=> /usr/local/lib/R/site-library/extrafontdb/metrics/LiberationSerif-Regular
Found FontName for 13 fonts.
Scanning afm files in /usr/local/lib/R/site-library/extrafontdb/metrics
Writing font table in /usr/local/lib/R/site-library/extrafontdb/fontmap/fonttable.csv
Writing Fontmap to /usr/local/lib/R/site-library/extrafontdb/fontmap/Fontmap...
excel_file_url = "https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3003260.s013&type=supplementary"
temp_file = tempfile(fileext = ".xlsx")
download.file(excel_file_url, destfile = temp_file, mode = "wb")
df1 = read_excel(temp_file, sheet = "2B", range = "B7:K55")head(df1)| Compound | Mode of action | EVC | acrABp | marRABp | micFp | ompFp | robp | soxSp | tolCp |
|---|---|---|---|---|---|---|---|---|---|
| <chr> | <chr> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> | <dbl> |
| Amikacin | Cidal | -3.700924e-16 | -0.05462461 | -0.023720165 | 0.24779952 | 0.07884039 | 0.04783275 | 0.30330932 | 0.326415371 |
| Amoxicillin | Cidal | 1.110223e-16 | 0.29424128 | 0.338067871 | 0.59177227 | -0.08126560 | 0.08376011 | 0.22395374 | 0.477010608 |
| Aztreonam | Cidal | -6.418477e-16 | -0.17941785 | -0.002771767 | -0.15203742 | 0.08483153 | -0.28280735 | 0.13645517 | 0.016670157 |
| Bacitracin | Cidal | -2.636780e-16 | -0.23245612 | -0.043469021 | -0.18737593 | 0.37846582 | -0.02473662 | -0.18525615 | -0.521333690 |
| Benzalkonium | Cidal | -1.480297e-16 | -0.36624844 | -0.326856765 | -0.26865357 | -0.71745534 | -0.85429358 | -0.15839416 | -0.089482819 |
| Cefaclor | Cidal | 2.405664e-16 | -0.10414697 | -0.121515539 | 0.01571115 | -0.06044260 | 0.07792023 | 0.05255932 | -0.001557381 |
print(temp_file)[1] "/tmp/RtmpIgmKoD/file9617cde6494.xlsx"df_longer = df1 |>
pivot_longer(
cols = -c('Compound','Mode of action'),
names_to = "variable",
values_to = "value"
)
head(df_longer)| Compound | Mode of action | variable | value |
|---|---|---|---|
| <chr> | <chr> | <chr> | <dbl> |
| Amikacin | Cidal | EVC | -3.700924e-16 |
| Amikacin | Cidal | acrABp | -5.462461e-02 |
| Amikacin | Cidal | marRABp | -2.372016e-02 |
| Amikacin | Cidal | micFp | 2.477995e-01 |
| Amikacin | Cidal | ompFp | 7.884039e-02 |
| Amikacin | Cidal | robp | 4.783275e-02 |
df_longer |>
ggplot(aes(x=`Mode of action`, y=value)) +
geom_point() +
theme_classic(base_size = 16)
ggplot(df_longer, aes(x = `Mode of action`, y = value, fill = `Mode of action`)) +
geom_violin(alpha = 0.5, color = NA) +
geom_boxplot(width = 0.1, alpha = 0.8, outlier.size = 2) +
theme_minimal() +
labs(
title = "Distribution of Values by Mode of Action",
x = "Mode of Action",
y = "Value"
) +
theme(legend.position = "none")
# To ensure consistent font rendering between Colab and saved files,
# it's best to register and use a common font family.
# First, import system fonts (run this once per session or if fonts change)
# font_import(paths = c("/usr/share/fonts/truetype/liberation"), prompt = FALSE) # Example for Liberation Sans
# fonts()
# loadfonts(device = "postscript") # For PDF output
# loadfonts(device = "win") # For Windows devices
loadfonts(device = "all") # Loads all fonts for all devices
# Define the function to calculate counts and position them
give_n <- function(x) {
return(data.frame(y = min(x, na.rm = TRUE) - 0.5, label = paste0("n = ", length(na.omit(x)))))
}
ggplot(df_longer, aes(x = `Mode of action`, y = value, fill = `Mode of action`)) +
geom_violin(alpha = 0.5, color = NA) +
geom_boxplot(width = 0.1, alpha = 0.8, outlier.size = 2) +
# Add counts at the bottom using stat_summary
stat_summary(fun.data = give_n, geom = "text",
position = position_dodge(0.9), size = 5, fontface = "bold") +
theme_minimal() +
labs(
title = "Distribution of mean Z-scores by Mode of Action",
x = "Antibiotic",
y = "Mean Z-scores"
) +
theme(
legend.position = "none",
# Specify a consistent font family for all text elements
text = element_text(family = "Liberation Sans"), # Explicitly use 'Liberation Sans'
# Increase size of the x-axis and y-axis labels (tick labels)
axis.text.x = element_text(size = 14, face = "bold"),
axis.text.y = element_text(size = 14, face = "bold"),
# Increase size of the axis titles
axis.title.x = element_text(size = 14, face = "bold", margin = margin(t = 10)),
axis.title.y = element_text(size = 14, face = "bold", margin = margin(r = 10)),
# Increase size of the plot title
plot.title = element_text(size = 16, face = "bold", hjust = 0.5)
)
ggsave("test1.png", dpi = 300)Humor Sans already registered with pdfFont(). Liberation Mono already registered with pdfFont(). Liberation Sans already registered with pdfFont(). Liberation Serif already registered with pdfFont(). Humor Sans already registered with postscriptFont(). Liberation Mono already registered with postscriptFont(). Liberation Sans already registered with postscriptFont(). Liberation Serif already registered with postscriptFont(). Saving 6.67 x 6.67 in image
