Figure 1
Anna Joachimbauer
2024-10-02
Last updated: 2026-03-03
Checks: 6 1
Knit directory: Serology Analysis/
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Load Packages
suppressPackageStartupMessages({
# Data handling
library(tidyverse)
library(data.table)
library(magrittr)
library(janitor)
library(here)
library(scales)
library(table1)
library(tableone)
library(flextable)
library(gtsummary)
library(openxlsx)
library(writexl)
library(readxl)
# Visualization
library(ggplot2)
library(ggpubr)
library(ggrepel)
library(ggbeeswarm)
library(ggcorrplot)
library(corrplot)
library(pheatmap)
library(ComplexHeatmap)
library(circlize)
library(RColorBrewer)
library(EnhancedVolcano)
library(plotly)
library(patchwork)
library(cowplot)
library(gridExtra)
library(grid)
library(ggpattern)
# Statistics
library(rstatix)
library(multcomp)
library(car)
library(Hmisc)
library(MASS)
library(MuMIn)
library(broom)
library(glmnet)
library(logistf)
library(drc)
library(caret)
library(mice)
library(pROC)
# Clustering
library(randomForest)
library(factoextra)
library(cluster)
library(Rtsne)
library(umap)
library(dbscan)
library(kernlab)
library(Seurat)
# Others
library(ImmunoLogic)
})Define Filepath
basedir <- here()Read Data (Cohort 1, Cohort 2)
table_clindat_cohort1 <- openxlsx::read.xlsx(file.path(basedir, "data", "Table_ClinicalData_Cohort1.xlsx")) %>%
dplyr::select(Study_ID, NTproBNP, LV_EF, Trop_I, CRP) %>%
mutate(Cohort = "Cohort1")
table_clindat_cohort2 <- openxlsx::read.xlsx(file.path(basedir, "data", "Table_ClinicalData_Cohort2.xlsx")) %>%
dplyr::select(Study_ID, NTproBNP, LV_EF, Trop_I, CRP) %>%
mutate(Cohort = "Cohort2")
table_cohorts <- rbind(table_clindat_cohort1 %>% dplyr::select(Study_ID, Cohort),
table_clindat_cohort2 %>% dplyr::select(Study_ID, Cohort))Multiple Imputation
# Combine data tables
table_clindat_myo <- rbind(table_clindat_cohort2 %>% dplyr::select(-Cohort),
table_clindat_cohort1 %>% dplyr::select(-Cohort))
# Impute missing values
imputed_data <- mice(table_clindat_myo, m = 5, method = 'pmm', maxit = 5, seed = 123)
iter imp variable
1 1 NTproBNP LV_EF Trop_I
1 2 NTproBNP LV_EF Trop_I
1 3 NTproBNP LV_EF Trop_I
1 4 NTproBNP LV_EF Trop_I
1 5 NTproBNP LV_EF Trop_I
2 1 NTproBNP LV_EF Trop_I
2 2 NTproBNP LV_EF Trop_I
2 3 NTproBNP LV_EF Trop_I
2 4 NTproBNP LV_EF Trop_I
2 5 NTproBNP LV_EF Trop_I
3 1 NTproBNP LV_EF Trop_I
3 2 NTproBNP LV_EF Trop_I
3 3 NTproBNP LV_EF Trop_I
3 4 NTproBNP LV_EF Trop_I
3 5 NTproBNP LV_EF Trop_I
4 1 NTproBNP LV_EF Trop_I
4 2 NTproBNP LV_EF Trop_I
4 3 NTproBNP LV_EF Trop_I
4 4 NTproBNP LV_EF Trop_I
4 5 NTproBNP LV_EF Trop_I
5 1 NTproBNP LV_EF Trop_I
5 2 NTproBNP LV_EF Trop_I
5 3 NTproBNP LV_EF Trop_I
5 4 NTproBNP LV_EF Trop_I
5 5 NTproBNP LV_EF Trop_I# Check the imputed data
print(densityplot(imputed_data, col=c("grey", "blue"), pch = c(1, 20)))
Warning! The custom
fig.path you set was
ignored by workflowr.
# Create a data set with the observed and completed data
table_imp <- complete(imputed_data, 1)
# Add Cohort
table_clindat_myo_imp <- merge (table_imp, table_cohorts, by = "Study_ID")Comparison routine clinical parameter between AM Cohorts
# Prepare data table
table_para <- table_clindat_myo_imp %>%
pivot_longer(cols = where(is.numeric),
names_to = "Parameter",
values_to = "Parameter_val")
# Calculate Stats
# Wilcox Test
stat.test <- table_para %>%
group_by(Parameter) %>%
wilcox_test(Parameter_val ~ Cohort) %>%
add_significance() %>%
mutate(p_adj = p.adjust(p, method = "BH"))
# Get max value per parameter (for p-value position)
max_y <- table_para %>%
group_by(Parameter) %>%
summarise(max_val = max(Parameter_val, na.rm = TRUE))
# Get min value per parameter (for y limits)
min_y <- table_para %>%
group_by(Parameter) %>%
summarise(min_val = min(Parameter_val, na.rm = TRUE))
# Combine with max_y info for plotting
stat.test <- stat.test %>%
left_join(max_y, by = "Parameter") %>%
left_join(min_y, by = "Parameter") %>%
mutate(y.position = max_val * 1.1)
# Create the loop to create a plot
param <- c("Trop_I", "CRP", "NTproBNP")
# Create x-axis label for loop
biomarker_labels <- c("Troponin I (ng/l)", "CRP (mg/l)", "NT-proBNP (ng/l)")
names(biomarker_labels) <- param
# Create a list for all plots created in the loop
plots_list <- list()
for (param in param)
{
# Filter for the data
temp_data <- table_para %>%
filter(Parameter == param)
temp_stat_test <- stat.test %>%
filter(Parameter == param) %>%
mutate(p_adj_label = ifelse(p_adj < 0.001, "<0.001", sprintf("%.3f", p_adj)))
# define y axis margins
max_y <- max(temp_stat_test$max_val, na.rm = TRUE) * 1.1
max_log10_limit <- 10^(ceiling(log10(max_y)))
min_y_limit <- min_y %>%
filter(Parameter == param) %>%
summarise(min_val = min(min_val, na.rm = TRUE) * 0.9) %>%
pull(min_val)
min_log10_limit <- 10^(floor(log10(min_y_limit)))
y_breaks <- 10^(seq(log10(min_log10_limit), log10(max_log10_limit), by = 1))
# Create Plot
plot_lum <- ggplot(temp_data, aes(x = Cohort, y = Parameter_val)) +
geom_boxplot(aes(fill = Cohort), color = "black", outlier.shape = NA,
width = 0.6, alpha = 0.4) +
geom_point(shape = 21, size = 3, color = "black", aes(fill = Cohort),
position = position_jitter(width = 0.2, height = 0)) +
scale_fill_manual(values = c("Cohort1" = "royalblue4",
"Cohort2" = "orange")) +
stat_pvalue_manual(temp_stat_test, label = "p_adj_label",
y.position = log10(temp_stat_test$y.position),
step.increase = 0.01, tip.length = 0) +
scale_y_log10(labels = function(x) format(x, scientific = FALSE, trim = TRUE),
limits = c(NA, max_log10_limit),
expand = expansion(mult = c(0.05, 0), add = c(0,0)), breaks = y_breaks) +
labs(x = NULL, y = biomarker_labels[param]) +
theme_classic() +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
legend.position = "none")
plots_list[[param]] <- plot_lum
}
# Create Plot LVEF
# Filter for the data
temp_data <- table_para %>%
filter(Parameter == "LV_EF")
temp_stat_test <- stat.test %>%
filter(Parameter == "LV_EF") %>%
mutate(p_adj_label = ifelse(p_adj < 0.001, "<0.001", sprintf("%.3f", p_adj)))
plot_lvef <- ggplot(temp_data, aes(x = Cohort, y = Parameter_val)) +
geom_boxplot(aes(fill = Cohort), color = "black", outlier.shape = NA,
width = 0.6, alpha = 0.4) +
geom_point(shape = 21, size = 3, color = "black", aes(fill = Cohort),
position = position_jitter(width = 0.2, height = 0)) +
scale_y_continuous(limits = c(0, 80), expand = c(0, 0)) +
scale_fill_manual(values = c("Cohort1" = "royalblue4",
"Cohort2" = "orange")) +
stat_pvalue_manual(temp_stat_test, label = "p_adj_label",
y.position = temp_stat_test$y.position,
step.increase = 0.01, tip.length = 0) +
labs(x = NULL, y = "LVEF (%)") +
theme_classic() +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
legend.position = "none")
# Combine plots to a panel
panel <- ggarrange(plotlist = c(plot_lvef, plots_list),
ncol = 4, nrow = 1,
common.legend = TRUE)
print(panel)
Warning! The custom
fig.path you set was
ignored by workflowr.
Correlation NTprobNP with routine blood marker
# Rename Datatables
table_corr <- table_clindat_myo_imp
# Define biomarkers
biomarkers <- c("Trop_I", "CRP")
# Define axis labels for each biomarker
biomarker_labels <- c("Troponin I (ng/l)", "CRP (mg/l)")
names(biomarker_labels) <- biomarkers
# Create list for plots
plots_list <- list()
# Loop Correlation Plot
for (p in biomarkers)
{
# Compute Spearman correlation
cor_test <- cor.test(table_corr$NTproBNP, table_corr[[p]], method = "spearman")
# Define x axis margins and breaks
max_x <- max(table_corr[[p]], na.rm = TRUE) * 1.1
min_x <- min(table_corr[[p]], na.rm = TRUE)
max_log10_limit <- 10^(ceiling(log10(max_x)))
min_log10_limit <- 10^(floor(log10(min_x)))
x_breaks <- 10^(seq(log10(min_log10_limit), log10(max_log10_limit), by = 1))
# Scatter plot with regression line
plot <- ggplot(table_corr, aes(x = .data[[p]], y = NTproBNP)) +
geom_point(shape = 21, size = 4, color = "black",
fill = "darkred",
position = position_jitter(width = 0.05, height = 0)) +
geom_smooth(method = "lm", se = TRUE, color = "black") +
scale_x_log10(labels = function(y) format(y, scientific = FALSE, trim = TRUE),
limits = c(min_log10_limit, max_log10_limit),
expand = c(0.1, 0), breaks = x_breaks) +
scale_y_log10(labels = function(x) format(x, scientific = FALSE, trim = TRUE),
limits = c(NA, 100000), expand = c(0.1, 0)) +
theme_classic() +
labs(x = biomarker_labels[[p]], y = "NT-proBNP (ng/l)") +
annotate("text", x = min(table_corr[[p]], na.rm = TRUE),
y = max(table_corr$LV_EF, na.rm = TRUE),
label = paste0("r = ", round(cor_test$estimate, 2),
"\np = ", ifelse(cor_test$p.value < 0.001, "< 0.001",signif(cor_test$p.value, 3))),
hjust = 0, vjust = 1, size = 6)
# Store each plot
plots_list[[p]] <- plot
}
# Combine plots to a panel
panel <- ggarrange(plotlist = plots_list,
ncol = 2, nrow = 1)
print(panel)
Warning! The custom
fig.path you set was
ignored by workflowr.
session info
sessionInfo()R version 4.4.3 (2025-02-28)
Platform: aarch64-apple-darwin20
Running under: macOS 26.3
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Zurich
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ImmunoLogic_0.0.0.9000 Seurat_5.3.1 SeuratObject_5.2.0
[4] sp_2.2-0 kernlab_0.9-33 dbscan_1.2-0
[7] umap_0.2.10.0 Rtsne_0.17 cluster_2.1.8
[10] factoextra_1.0.7 randomForest_4.7-1.2 pROC_1.19.0.1
[13] mice_3.18.0 caret_7.0-1 lattice_0.22-6
[16] drc_3.0-1 logistf_1.26.1 glmnet_4.1-10
[19] Matrix_1.7-2 broom_1.0.11 MuMIn_1.48.11
[22] Hmisc_5.2-3 car_3.1-3 carData_3.0-5
[25] multcomp_1.4-28 TH.data_1.1-4 MASS_7.3-65
[28] survival_3.8-3 mvtnorm_1.3-3 rstatix_0.7.3
[31] ggpattern_1.2.1 gridExtra_2.3 cowplot_1.2.0
[34] patchwork_1.3.2 plotly_4.11.0 EnhancedVolcano_1.24.0
[37] RColorBrewer_1.1-3 circlize_0.4.16 ComplexHeatmap_2.22.0
[40] pheatmap_1.0.12 corrplot_0.95 ggcorrplot_0.1.4.1
[43] ggbeeswarm_0.7.2 ggrepel_0.9.6 ggpubr_0.6.2
[46] readxl_1.4.5 writexl_1.5.0 openxlsx_4.2.5.2
[49] gtsummary_2.4.0 flextable_0.9.6 tableone_0.13.2
[52] table1_1.4.3 scales_1.4.0 here_1.0.2
[55] janitor_2.2.0 magrittr_2.0.4 data.table_1.17.8
[58] lubridate_1.9.4 forcats_1.0.1 stringr_1.6.0
[61] dplyr_1.1.4 purrr_1.2.0 readr_2.1.6
[64] tidyr_1.3.1 tibble_3.3.0 ggplot2_4.0.1
[67] tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] IRanges_2.40.1 nnet_7.3-20 goftest_1.2-3
[4] vctrs_0.6.5 spatstat.random_3.4-3 digest_0.6.39
[7] png_0.1-8 shape_1.4.6.1 git2r_0.36.2
[10] alabama_2023.1.0 deldir_2.0-4 httpcode_0.3.0
[13] parallelly_1.45.1 fontLiberation_0.1.0 reshape2_1.4.5
[16] httpuv_1.6.16 foreach_1.5.2 BiocGenerics_0.52.0
[19] withr_3.0.2 xfun_0.54 crul_1.4.2
[22] emmeans_1.10.4 systemfonts_1.3.1 ragg_1.5.0
[25] zoo_1.8-14 GlobalOptions_0.1.3 gtools_3.9.5
[28] pbapply_1.7-4 Formula_1.2-5 promises_1.5.0
[31] otel_0.2.0 httr_1.4.7 globals_0.18.0
[34] fitdistrplus_1.2-4 rstudioapi_0.17.1 pan_1.9
[37] miniUI_0.1.2 generics_0.1.4 base64enc_0.1-3
[40] curl_7.0.0 S4Vectors_0.44.0 mitools_2.4
[43] polyclip_1.10-7 quadprog_1.5-8 xtable_1.8-4
[46] doParallel_1.0.17 evaluate_1.0.5 hms_1.1.4
[49] irlba_2.3.5.1 colorspace_2.1-2 polynom_1.4-1
[52] ROCR_1.0-11 reticulate_1.44.1 spatstat.data_3.1-9
[55] lmtest_0.9-40 snakecase_0.11.1 later_1.4.4
[58] spatstat.geom_3.6-1 future.apply_1.20.0 scattermore_1.2
[61] survey_4.4-2 matrixStats_1.5.0 RcppAnnoy_0.0.22
[64] class_7.3-23 pillar_1.11.1 nlme_3.1-167
[67] iterators_1.0.14 compiler_4.4.3 RSpectra_0.16-2
[70] stringi_1.8.7 gower_1.0.2 jomo_2.7-6
[73] tensor_1.5.1 minqa_1.2.8 plyr_1.8.9
[76] crayon_1.5.3 abind_1.4-8 orthopolynom_1.0-6.1
[79] sandwich_3.1-1 codetools_0.2-20 textshaping_1.0.4
[82] basefun_1.2-4 recipes_1.3.1 openssl_2.3.4
[85] bslib_0.9.0 GetoptLong_1.0.5 mime_0.13
[88] splines_4.4.3 Rcpp_1.1.0 fastDummies_1.7.5
[91] coneproj_1.20 variables_1.1-2 cellranger_1.1.0
[94] knitr_1.50 clue_0.3-66 lme4_1.1-38
[97] fs_1.6.6 listenv_0.10.0 checkmate_2.3.3
[100] Rdpack_2.6.4 ggsignif_0.6.4 estimability_1.5.1
[103] tzdb_0.5.0 pkgconfig_2.0.3 tools_4.4.3
[106] cachem_1.1.0 rbibutils_2.4 numDeriv_2016.8-1.1
[109] viridisLite_0.4.2 DBI_1.2.3 fastmap_1.2.0
[112] rmarkdown_2.30 ica_1.0-3 tram_1.2-4
[115] sass_0.4.10 officer_0.6.6 coda_0.19-4.1
[118] dotCall64_1.2 RANN_2.6.2 rpart_4.1.24
[121] farver_2.1.2 reformulas_0.4.2 mgcv_1.9-1
[124] yaml_2.3.11 workflowr_1.7.2 foreign_0.8-88
[127] cli_3.6.5 stats4_4.4.3 lifecycle_1.0.4
[130] uwot_0.2.4 askpass_1.2.1 lava_1.8.0
[133] backports_1.5.0 mlt_1.6-6 timechange_0.3.0
[136] gtable_0.3.6 rjson_0.2.23 ggridges_0.5.7
[139] progressr_0.18.0 parallel_4.4.3 jsonlite_2.0.0
[142] RcppHNSW_0.6.0 mitml_0.4-5 qrng_0.0-10
[145] spatstat.utils_3.2-0 zip_2.3.1 jquerylib_0.1.4
[148] spatstat.univar_3.1-5 timeDate_4051.111 lazyeval_0.2.2
[151] shiny_1.12.0 htmltools_0.5.9 sctransform_0.4.2
[154] glue_1.8.0 gfonts_0.2.0 BB_2019.10-1
[157] spam_2.11-1 gdtools_0.3.7 rprojroot_2.1.1
[160] boot_1.3-31 igraph_2.2.1 R6_2.6.1
[163] labeling_0.4.3 ipred_0.9-15 nloptr_2.2.1
[166] tidyselect_1.2.1 vipor_0.4.7 plotrix_3.8-4
[169] htmlTable_2.4.3 operator.tools_1.6.3 xml2_1.5.1
[172] fontBitstreamVera_0.1.1 future_1.68.0 ModelMetrics_1.2.2.2
[175] KernSmooth_2.23-26 S7_0.2.1 fontquiver_0.2.1
[178] htmlwidgets_1.6.4 rlang_1.1.6 spatstat.sparse_3.1-0
[181] spatstat.explore_3.6-0 uuid_1.2-1 formula.tools_1.7.1
[184] hardhat_1.4.1 beeswarm_0.4.0 prodlim_2023.08.28 date()[1] "Tue Mar 3 16:55:08 2026"
sessionInfo()R version 4.4.3 (2025-02-28)
Platform: aarch64-apple-darwin20
Running under: macOS 26.3
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Zurich
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ImmunoLogic_0.0.0.9000 Seurat_5.3.1 SeuratObject_5.2.0
[4] sp_2.2-0 kernlab_0.9-33 dbscan_1.2-0
[7] umap_0.2.10.0 Rtsne_0.17 cluster_2.1.8
[10] factoextra_1.0.7 randomForest_4.7-1.2 pROC_1.19.0.1
[13] mice_3.18.0 caret_7.0-1 lattice_0.22-6
[16] drc_3.0-1 logistf_1.26.1 glmnet_4.1-10
[19] Matrix_1.7-2 broom_1.0.11 MuMIn_1.48.11
[22] Hmisc_5.2-3 car_3.1-3 carData_3.0-5
[25] multcomp_1.4-28 TH.data_1.1-4 MASS_7.3-65
[28] survival_3.8-3 mvtnorm_1.3-3 rstatix_0.7.3
[31] ggpattern_1.2.1 gridExtra_2.3 cowplot_1.2.0
[34] patchwork_1.3.2 plotly_4.11.0 EnhancedVolcano_1.24.0
[37] RColorBrewer_1.1-3 circlize_0.4.16 ComplexHeatmap_2.22.0
[40] pheatmap_1.0.12 corrplot_0.95 ggcorrplot_0.1.4.1
[43] ggbeeswarm_0.7.2 ggrepel_0.9.6 ggpubr_0.6.2
[46] readxl_1.4.5 writexl_1.5.0 openxlsx_4.2.5.2
[49] gtsummary_2.4.0 flextable_0.9.6 tableone_0.13.2
[52] table1_1.4.3 scales_1.4.0 here_1.0.2
[55] janitor_2.2.0 magrittr_2.0.4 data.table_1.17.8
[58] lubridate_1.9.4 forcats_1.0.1 stringr_1.6.0
[61] dplyr_1.1.4 purrr_1.2.0 readr_2.1.6
[64] tidyr_1.3.1 tibble_3.3.0 ggplot2_4.0.1
[67] tidyverse_2.0.0
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[4] vctrs_0.6.5 spatstat.random_3.4-3 digest_0.6.39
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[13] parallelly_1.45.1 fontLiberation_0.1.0 reshape2_1.4.5
[16] httpuv_1.6.16 foreach_1.5.2 BiocGenerics_0.52.0
[19] withr_3.0.2 xfun_0.54 crul_1.4.2
[22] emmeans_1.10.4 systemfonts_1.3.1 ragg_1.5.0
[25] zoo_1.8-14 GlobalOptions_0.1.3 gtools_3.9.5
[28] pbapply_1.7-4 Formula_1.2-5 promises_1.5.0
[31] otel_0.2.0 httr_1.4.7 globals_0.18.0
[34] fitdistrplus_1.2-4 rstudioapi_0.17.1 pan_1.9
[37] miniUI_0.1.2 generics_0.1.4 base64enc_0.1-3
[40] curl_7.0.0 S4Vectors_0.44.0 mitools_2.4
[43] polyclip_1.10-7 quadprog_1.5-8 xtable_1.8-4
[46] doParallel_1.0.17 evaluate_1.0.5 hms_1.1.4
[49] irlba_2.3.5.1 colorspace_2.1-2 polynom_1.4-1
[52] ROCR_1.0-11 reticulate_1.44.1 spatstat.data_3.1-9
[55] lmtest_0.9-40 snakecase_0.11.1 later_1.4.4
[58] spatstat.geom_3.6-1 future.apply_1.20.0 scattermore_1.2
[61] survey_4.4-2 matrixStats_1.5.0 RcppAnnoy_0.0.22
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[67] iterators_1.0.14 compiler_4.4.3 RSpectra_0.16-2
[70] stringi_1.8.7 gower_1.0.2 jomo_2.7-6
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[142] RcppHNSW_0.6.0 mitml_0.4-5 qrng_0.0-10
[145] spatstat.utils_3.2-0 zip_2.3.1 jquerylib_0.1.4
[148] spatstat.univar_3.1-5 timeDate_4051.111 lazyeval_0.2.2
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[175] KernSmooth_2.23-26 S7_0.2.1 fontquiver_0.2.1
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[181] spatstat.explore_3.6-0 uuid_1.2-1 formula.tools_1.7.1
[184] hardhat_1.4.1 beeswarm_0.4.0 prodlim_2023.08.28