Last updated: 2021-02-19

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Knit directory: melanoma_publication_old_data/

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Introduction

This script generates plots for Supplementary Figure 4.

Preparations

Load libraries

First, we will load the libraries needed for this part of the analysis.

sapply(list.files("code/helper_functions", full.names = TRUE), source)
        code/helper_functions/calculateSummary.R
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        code/helper_functions/censor_dat.R
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        code/helper_functions/detect_mRNA_expression.R
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        code/helper_functions/DistanceToClusterCenter.R
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visible FALSE                                          
        code/helper_functions/findMilieu.R code/helper_functions/findPatch.R
value   ?                                  ?                                
visible FALSE                              FALSE                            
        code/helper_functions/getInfoFromString.R
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        code/helper_functions/getSpotnumber.R
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        code/helper_functions/plotCellCounts.R
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        code/helper_functions/plotCellFractions.R
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        code/helper_functions/plotDist.R
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        code/helper_functions/scatter_function.R
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        code/helper_functions/sceChecks.R
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        code/helper_functions/validityChecks.R
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visible FALSE                                 
library(SingleCellExperiment)
library(reshape2)
library(tidyverse)
library(dplyr)
library(data.table) 
library(ggplot2)
library(ComplexHeatmap)
library(rms)
library(ggrepel)
library(ggbeeswarm)
library(circlize)
library(ggpubr)
library(ggridges)
library(gridExtra)
library(rstatix)

Read the data

sce_rna = readRDS(file = "data/data_for_analysis/sce_RNA.rds")
sce_prot = readRDS(file = "data/data_for_analysis/sce_protein.rds")

Supp Figure 4A

Heatmap showing marker expression of celltypes subclusters

# add marker expression to cells
marker_expression <- data.frame(t(assay(sce_prot[rowData(sce_prot)$good_marker,], "asinh")))
marker_expression$cellID <- rownames(marker_expression)
dat <- data.frame(colData(sce_prot))[,c("cellID", "celltype_clustered")]
dat <- left_join(dat, marker_expression)
Joining, by = "cellID"
dat$cellID <- NULL

# aggregate the groups
dat_aggr <- dat %>%
  group_by(celltype_clustered) %>%
  summarise_all(funs(mean))
Warning: `funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
# number of cells per group
dat_sum <- dat %>%
  group_by(celltype_clustered) %>%
  summarise(n=n())
`summarise()` ungrouping output (override with `.groups` argument)
dat_sum <- data.frame(t(dat_sum))

# scale and center expression
dat_aggr[,-c(1)] <- scale(dat_aggr[,-c(1)])

# create matrix
m <- as.matrix(t(dat_aggr[,-c(1)]))
colnames(m) <- dat_aggr$celltype_clustered

# top annotation with number of cells
ha <- HeatmapAnnotation("Number of Cells" = anno_barplot(ifelse(as.numeric(dat_sum[2,])>25000, 25100, as.numeric(dat_sum[2,])),
                                                         height = unit(2,"cm"),
                                                         ylim = range(0,25000),
                                                         gp = gpar(fill = ifelse(as.numeric(dat_sum[2,]) > 25000, "white", "black"),
                                                                   col = "white")),
                        "Numbers" = anno_text(round(as.numeric(dat_sum[2,])), 
                                                   which = "column", 
                                                   rot = 90, 
                                                   just = "center", 
                                                   location = 0.5,
                                                   gp = gpar(fontsize=8,col = ifelse(as.numeric(dat_sum[2,]) > 25000, "red", "black"))))

# row_split for markers
rowData(sce_prot)$heatmap_relevance <- ""
rowData(sce_prot[rowData(sce_prot)$good_marker,])$heatmap_relevance <- "lineage"
rowData(sce_prot[grepl("PDL1|CD11b|CD206|PARP|CXCR2|CD11c|pS6|GrzB|IDO1|CD45RA|H3K27me3|TCF7|CD45RO|PD1|pERK|ICOS|Ki67", rownames(sce_prot)),])$heatmap_relevance <- "other"

# plot heatmap
h <- Heatmap(m, name = "Scaled Expression",
             row_split = rowData(sce_prot[rowData(sce_prot)$good_marker,])$heatmap_relevance,
             cluster_columns = FALSE,
             show_column_dend = FALSE,
             column_names_gp = gpar(fontsize=12),
             column_names_rot = 90,
             column_names_centered = TRUE,
             show_column_names = TRUE,
             top_annotation = ha,
             col = colorRamp2(c(-3, 0, 3), c("blue", "white", "red")),
             heatmap_legend_param = list(at = c(-3:3),legend_width = unit(6,"cm"), direction="horizontal"),
             column_names_side = "top",
             height = unit(20, "cm"),
             width = unit(20,"cm"))

draw(h, heatmap_legend_side = "bottom")

Supp Figure 4B

Tumor Marker Profile for different Dysfunction Scoring Groups per Image

tumor_marker_protein <- c("pS6", "bCatenin", "H3K27me3", "HLADR", "Sox9", "pERK", "p75", "PDL1", "Ki67", "SOX10", "PARP")
tumor_marker_rna <- c("B2M")

# rna data 
dat_rna <- data.frame(t(assay(sce_rna[tumor_marker_rna, sce_rna$celltype == "Tumor"], "asinh")))
dat_rna$cellID <- rownames(dat_rna)
dat_rna <- left_join(dat_rna, data.frame(colData(sce_rna))[,c("cellID", "dysfunction_score", "Description", "MM_location")])
Joining, by = "cellID"
# filter
dat_rna <- dat_rna %>%
  filter(dysfunction_score %in% c("high dysfunction", "low dysfunction"))

# mean per image
dat_rna <- dat_rna %>%
  select(-cellID) %>%
  group_by(Description, dysfunction_score) %>%
  summarise_if(is.numeric, mean, na.rm = TRUE)

# melt
dat_rna <- dat_rna %>%
  reshape2::melt(id.vars = c("Description", "dysfunction_score"), variable.name = "channel", value.name = "asinh")

# protein data
dat_prot <- data.frame(t(assay(sce_prot[tumor_marker_protein,, sce_prot$celltype == "Tumor"], "asinh")))
dat_prot$cellID <- rownames(dat_prot)
dat_prot <- left_join(dat_prot, data.frame(colData(sce_prot))[,c("cellID", "dysfunction_score", "Description", "MM_location")])
Joining, by = "cellID"
# filter
dat_prot <- dat_prot %>%
  filter(dysfunction_score %in% c("high dysfunction", "low dysfunction"))

# mean per image
dat_prot <- dat_prot %>%
  select(-cellID) %>%
  group_by(Description, dysfunction_score) %>%
  summarise_if(is.numeric, mean, na.rm = TRUE)

# melt
dat_prot <- dat_prot %>%
  reshape2::melt(id.vars = c("Description", "dysfunction_score"), variable.name = "channel", value.name = "asinh")

# join both data sets
comb <- rbind(dat_prot, dat_rna)

stat.test <- comb %>%
  group_by(channel) %>%
  wilcox_test(data = ., asinh ~ dysfunction_score) %>%
  adjust_pvalue(method = "BH") %>%
  add_significance("p.adj",cutpoints = c(0, 1e-04, 0.001, 0.01, 0.1, 1)) %>%
  add_xy_position(x = "celltype", dodge = 0.8)


# plot 
p <- ggplot(comb, aes(x=dysfunction_score, y=asinh)) + 
  geom_boxplot(alpha=0.2, lwd=1, aes(fill=dysfunction_score)) +
  geom_quasirandom(alpha=0.6, size=2, aes(col=dysfunction_score)) +
  scale_color_discrete(guide = FALSE) +
  theme_bw() +
  theme(text = element_text(size=18),
        axis.text.x = element_blank(),
        axis.ticks = element_blank(),
        axis.title.x = element_blank()) +
  facet_wrap(~channel, scales = "free", ncol = 3) + 
  stat_pvalue_manual(stat.test, label = "p.adj.signif", size = 7) + 
  xlab("") + 
  ylab("Mean Count per Image (asinh)") +
  scale_y_continuous(expand = expansion(mult = c(0.05, 0.2))) +
  guides(fill=guide_legend(title="Dysfunction Score", override.aes = c(lwd=0.5, alpha=1)))

leg <- get_legend(p)

grid.arrange(p + theme(legend.position = "none"))
grid.arrange(leg)

Supp Figure 4C

Define S100+ cells

y <- c(rep(1:10,16),rep(11,7))

# add the group information to the sce object
sce_rna$groups <- y[colData(sce_rna)$ImageNumber]

# now we use the function written by Nils
plotDist(sce_rna["S100", sce_rna$celltype == "Tumor"], plot_type = "ridges", 
         colour_by = "groups", split_by = "rows", 
         exprs_values = "asinh") +
  geom_vline(xintercept = 3)
# manual gating 
sce_rna$S100 <- ifelse(assay(sce_rna["S100",], "asinh") > 3, "positive", "negative")

# fraction of S100 tumor cells per image
s100 <- data.frame(colData(sce_rna)) %>%
  filter(celltype == "Tumor") %>%
  group_by(ImageNumber, dysfunction_score, S100) %>%
  summarise(n=n()) %>%
  mutate(fraction = n/sum(n)) %>%
  filter(is.na(dysfunction_score) == F & S100 == "positive")
`summarise()` regrouping output by 'ImageNumber', 'dysfunction_score' (override with `.groups` argument)
s100$dysfunction_score <- factor(s100$dysfunction_score)

stat.test <- s100 %>%
  group_by(S100) %>%
  wilcox_test(data = ., fraction ~ dysfunction_score) %>%
  adjust_pvalue(method = "BH") %>%
  add_significance("p.adj",cutpoints = c(0, 1e-04, 0.001, 0.01, 0.1, 1)) %>%
  add_x_position(dodge = 0.8)

ggplot(s100, aes(x=dysfunction_score, y=fraction)) + 
  geom_boxplot(alpha=0.2, lwd=1.5, aes(fill = dysfunction_score)) + 
  geom_quasirandom(aes(col=dysfunction_score), size=3) +
  stat_pvalue_manual(stat.test, label = "p.adj.signif", size = 7, y.position = 1) + 
  xlab("") + 
  ylab("Fraction of S100+ Tumor Cells") +
  theme_bw() +
  theme(text = element_text(size=16),
        legend.position = "none") +
  ylim(0,1.05)

Supp Figure 4D

Heatmap with Community Modules

cur_dt <- data.frame(colData(sce_rna))
clust <- data.frame()

## wide table for communities 
for(i in names(cur_dt[,grepl(glob2rx("*pure"),names(cur_dt))])) {
  cur_dt_sub <- cur_dt[cur_dt[,i] > 0,]
  cur_dt_sub <- cbind(cur_dt_sub[,c(i, "Description")],
                      cur_dt_sub[,grepl(glob2rx("C*L*"),names(cur_dt_sub))])
  
  # count numbers of chemokine-expressing cells per patch
  cur_dt_sub <- cur_dt_sub %>%
    group_by(Description) %>%
    group_by_at(i, .add = TRUE) %>%
    summarise_each(funs(sum))
  
  cur_dt_sub$cluster_type <- i
  
  cur_dt_sub <- cur_dt_sub[,-2]
  
  clust <- rbind(clust, cur_dt_sub)
}
Warning: `summarise_each_()` is deprecated as of dplyr 0.7.0.
Please use `across()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
# remove pure clusters with low abundance (CCL22, CCL4, CCL8)
clust <- clust[!(clust$cluster_type %in% c("ccl22_pure", "ccl4_pure", "ccl8_pure")),]

# number of patches by image
clust <- clust %>%
  group_by(Description, cluster_type) %>%
  summarise(n=n()) %>%
  reshape2::dcast(Description ~ cluster_type, value.var = "n", fill = 0)
`summarise()` regrouping output by 'Description' (override with `.groups` argument)
# add images with 0 clusters and add more information
to_add <- data.frame(colData(sce_rna)) %>%
  distinct(Description, .keep_all = TRUE)

clust <- left_join(to_add[,c("Description", "dysfunction_score", "Tcell_density_score_image")], clust)
Joining, by = "Description"
# repalce NA with 0 
cur_dt_wide <- clust %>%
  mutate_if(is.numeric,coalesce,0)

# order according to image infiltration score
cur_dt_wide <- cur_dt_wide[order(cur_dt_wide$dysfunction_score),]

# chemokines per image
total_chemokines <- cur_dt %>%
  group_by(Description, chemokine) %>%
  summarise(n=n()) %>%
  group_by(Description) %>%
  mutate(fraction = n/sum(n)) %>%
  filter(chemokine == TRUE)
`summarise()` regrouping output by 'Description' (override with `.groups` argument)
# is a expressing cell part of a milieu?
cur_dt$in_community <- ifelse(rowSums(cur_dt[,grepl(glob2rx("*pure"),names(cur_dt))]) > 0 & cur_dt$chemokine == TRUE, TRUE, FALSE)

# fraction in_community 1vs.0 per image
fractions <- cur_dt %>%
  filter(chemokine == TRUE) %>%
  group_by(Description, in_community) %>%
  summarise(n=n()) %>%
  group_by(Description) %>%
  mutate(fraction = n / sum(n)) %>%
  reshape2::dcast(Description ~ in_community, value.var = "fraction", fill = 0)
`summarise()` regrouping output by 'Description' (override with `.groups` argument)
names(fractions)[2:3] <- c("single", "community")
fractions[, 2:3][is.na(fractions[, 2:3])] <- 0

# chemokines per image (regardless of combination, multi-producing cells count more than once)
chemokines <- cbind(cur_dt[,c("Description", "in_community")], cur_dt[,grepl(glob2rx("C*L*"),names(cur_dt))])

# long table - chemokine / in_community info and count (n) per image
chemokines <- reshape2::melt(chemokines, id.vars = c("Description", "in_community"), variable.name = "chemokine", value.name = "n") %>%
  group_by(Description, in_community, chemokine) %>%
  summarise(total = sum(n)) %>%
  reshape2::dcast(Description + chemokine ~ in_community, value.var = "total") %>%
  replace(is.na(.), 0) %>%
  reshape2::melt(id.vars = c("Description", "chemokine"), variable.name = "in_community", value.name = "n")
`summarise()` regrouping output by 'Description', 'in_community' (override with `.groups` argument)
# combine all information
cur_dt_wide <- left_join(cur_dt_wide, fractions)
Joining, by = "Description"
cur_dt_wide <- left_join(cur_dt_wide, total_chemokines)
Joining, by = "Description"

Plot Heatmap

# remove controls and only keep images with dysfunction score
cur_dt_wide_sub <- cur_dt_wide[cur_dt_wide$Description %in% unique(sce_rna[,sce_rna$Location != "CTRL"]$Description),]
cur_dt_wide_sub <- cur_dt_wide[cur_dt_wide$dysfunction_score %in% c("high dysfunction", "low dysfunction"),]

# define subgroups to split  heatmap
subgroup = cur_dt_wide_sub[,"dysfunction_score"]

# heatmap annotation
row_ha2 = rowAnnotation("Production Mode of\nChemokine-Expressing Cells" = 
                          anno_barplot(cur_dt_wide_sub[,c("single", "community")], 
                                       gp = gpar(fill = c("#F8766D", "#00BFC4")), width = unit(1.5, "cm")),
                        "Fraction of Chemokine- \n Expressing Cells" = 
                          anno_barplot(cur_dt_wide_sub[,"fraction"],
                                       width = unit(1.5, "cm")),
                        annotation_name_rot = 90, gap = unit(3, "mm"),
                        col = list(Relapse = c("no relapse" = "orange", "relapse" = "black", "untreated/lost" = "grey")))

# function for the zoom-in plot
panel_fun_chemokines = function(index, nm) {
    image_number = cur_dt_wide_sub[index,"Description"]
    if(length(unique(image_number)) > 9){
      df = chemokines[chemokines$Description %in% image_number, ]
      g = ggplot(df, aes(x = factor(chemokine), y = log10(n+1), fill=in_community)) + 
        geom_boxplot() + 
        xlab("Chemokine") + 
        ylab("# Cells [log10(n+1)]") +
        theme_bw() +
        theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
              legend.position = "none") +
        ylim(0,3)
      g = grid.grabExpr(print(g))
      pushViewport(viewport())
      grid.rect()
      grid.draw(g)
      popViewport()
    }
}

# create zoom-in 
zoom = anno_zoom(align_to = subgroup, 
                 which = "row", panel_fun = panel_fun_chemokines, 
                 size = unit(6, "cm"), 
                 gap = unit(1, "cm"), 
                 width = unit(10, "cm"))

# heatmap
m <- as.matrix(cur_dt_wide_sub[,grepl(glob2rx("*pure"),names(cur_dt_wide_sub))])
col_names <- c()
for(i in (1:length(colnames(m)))){col_names <- c(col_names,(toupper(str_split(colnames(m), "_")[[i]][1])))}
colnames(m) <- col_names

col_fun = viridis::inferno(max(m)+1)

ht1 = Heatmap(m, 
        col = col_fun,
        left_annotation = row_ha2,
        right_annotation = rowAnnotation(foo = zoom, gap = unit(3,"cm")),
        row_split = subgroup,
        row_title_side = "left",
        border = T,
        row_gap = unit(3, "mm"),
        cluster_rows = T,
        cluster_columns = F,
        cluster_row_slices = F,
        show_heatmap_legend = F,
        show_row_dend = F,
        name = "Detected Patches",
        column_title = "Chemokine Milieu", 
        column_title_side = "bottom",
        column_title_gp = gpar(fontsize=20),
        show_row_names = F,
        width = unit(15,"cm"))

draw(ht1)
Warning: Removed 1 rows containing non-finite values (stat_boxplot).
# manual legends
lgd1 = Legend(labels = c("Stand-alone", "Milieu"), title = "Production Mode", legend_gp = gpar(fill = c("#F8766D", "#00BFC4")))
lgd2 = Legend(col_fun = colorRamp2(c(0:max(m)), colors = col_fun), 
              at = seq(0, max(m)+2, by=5), title = "Detected Milieus", direction = "horizontal", grid_width = unit(2, "cm"))

# Draw Legend
draw(packLegend(lgd2, lgd1, direction = "horizontal"))

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
 [1] rstatix_0.6.0               gridExtra_2.3              
 [3] ggridges_0.5.3              ggpubr_0.4.0               
 [5] circlize_0.4.12             ggbeeswarm_0.6.0           
 [7] ggrepel_0.9.0               rms_6.1-0                  
 [9] SparseM_1.78                Hmisc_4.4-2                
[11] Formula_1.2-4               survival_3.2-7             
[13] lattice_0.20-41             ComplexHeatmap_2.4.3       
[15] data.table_1.13.6           forcats_0.5.0              
[17] stringr_1.4.0               dplyr_1.0.2                
[19] purrr_0.3.4                 readr_1.4.0                
[21] tidyr_1.1.2                 tibble_3.0.4               
[23] ggplot2_3.3.3               tidyverse_1.3.0            
[25] reshape2_1.4.4              SingleCellExperiment_1.12.0
[27] SummarizedExperiment_1.20.0 Biobase_2.50.0             
[29] GenomicRanges_1.42.0        GenomeInfoDb_1.26.2        
[31] IRanges_2.24.1              S4Vectors_0.28.1           
[33] BiocGenerics_0.36.0         MatrixGenerics_1.2.0       
[35] matrixStats_0.57.0          workflowr_1.6.2            

loaded via a namespace (and not attached):
  [1] readxl_1.3.1           backports_1.2.1        plyr_1.8.6            
  [4] splines_4.0.3          TH.data_1.0-10         digest_0.6.27         
  [7] htmltools_0.5.0        viridis_0.5.1          fansi_0.4.1           
 [10] magrittr_2.0.1         checkmate_2.0.0        cluster_2.1.0         
 [13] openxlsx_4.2.3         modelr_0.1.8           sandwich_3.0-0        
 [16] jpeg_0.1-8.1           colorspace_2.0-0       rvest_0.3.6           
 [19] haven_2.3.1            xfun_0.20              crayon_1.3.4          
 [22] RCurl_1.98-1.2         jsonlite_1.7.2         zoo_1.8-8             
 [25] glue_1.4.2             gtable_0.3.0           zlibbioc_1.36.0       
 [28] XVector_0.30.0         MatrixModels_0.4-1     GetoptLong_1.0.5      
 [31] DelayedArray_0.16.0    car_3.0-10             shape_1.4.5           
 [34] abind_1.4-5            scales_1.1.1           mvtnorm_1.1-1         
 [37] DBI_1.1.0              Rcpp_1.0.5             viridisLite_0.3.0     
 [40] htmlTable_2.1.0        clue_0.3-58            foreign_0.8-81        
 [43] htmlwidgets_1.5.3      httr_1.4.2             RColorBrewer_1.1-2    
 [46] ellipsis_0.3.1         farver_2.0.3           pkgconfig_2.0.3       
 [49] nnet_7.3-14            dbplyr_2.0.0           labeling_0.4.2        
 [52] tidyselect_1.1.0       rlang_0.4.10           later_1.1.0.1         
 [55] munsell_0.5.0          cellranger_1.1.0       tools_4.0.3           
 [58] cli_2.2.0              generics_0.1.0         broom_0.7.3           
 [61] evaluate_0.14          yaml_2.2.1             knitr_1.30            
 [64] fs_1.5.0               zip_2.1.1              nlme_3.1-151          
 [67] whisker_0.4            quantreg_5.82          xml2_1.3.2            
 [70] compiler_4.0.3         rstudioapi_0.13        beeswarm_0.2.3        
 [73] curl_4.3               png_0.1-7              ggsignif_0.6.0        
 [76] reprex_0.3.0           stringi_1.5.3          Matrix_1.3-2          
 [79] vctrs_0.3.6            pillar_1.4.7           lifecycle_0.2.0       
 [82] GlobalOptions_0.1.2    bitops_1.0-6           conquer_1.0.2         
 [85] httpuv_1.5.4           R6_2.5.0               latticeExtra_0.6-29   
 [88] promises_1.1.1         rio_0.5.16             vipor_0.4.5           
 [91] codetools_0.2-18       polspline_1.1.19       MASS_7.3-53           
 [94] assertthat_0.2.1       rprojroot_2.0.2        rjson_0.2.20          
 [97] withr_2.3.0            multcomp_1.4-15        GenomeInfoDbData_1.2.4
[100] hms_0.5.3              rpart_4.1-15           rmarkdown_2.6         
[103] carData_3.0-4          git2r_0.28.0           lubridate_1.7.9.2     
[106] base64enc_0.1-3