Pre-processing kinobeads data
Junyan Lu
2021-10-05
Last updated: 2022-01-06
Checks: 6 1
Knit directory: DepInfeR/analysis/
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Load packages
Packages
library(readxl)
library(tidyverse)
source("../code/utils.R")Read data sets
The drug-target data can be found in the supplementary file of the paper (Table_S1 & Table_S2): https://science.sciencemag.org/content/358/6367/eaan4368/tab-figures-data
# kinase inhibitor drug-target screen from supplementary tables (Table_S1 & Table_S2)
tarList <- read_xlsx("../data/kinobeads/Klaeger_allTargets.xlsx", sheet = "Kinobeads")
tarList_syn <- read_xlsx("../data/kinobeads/targets_pubchem.xlsx", sheet = "Inhibitor annotation", col_names = TRUE) Preprocess dataset
Attach synonyms to target table
tarList$synonyms <- tarList_syn$Synonyms[match(tarList$Drug, tarList_syn$Drug)]Process drug names of target table
#use lowercase
tarList <- mutate(tarList, Drug = tolower(Drug)) %>%
mutate(Drug = gsub("[- ]","", Drug))
#change pd325901 to pd0325901 (due to different naming)
tarList[tarList$Drug == "pd325901",]$Drug <- "pd0325901"Rename BCR to BCR/ABL to avoid confusion with B-cell receptor (BCR)
tarList <- mutate(tarList, `Gene Name` = ifelse(`Gene Name` %in% "BCR", "BCR/ABL", `Gene Name`))Plot distributions of drugs and targe kinases
Kinases per drug
plotTab <- tarList %>% filter(`Target Classification` =="High confidence") %>%
group_by(Drug) %>% summarise(nTar = length(`Gene Name`))
p1 <- ggplot(plotTab, aes(x=nTar)) + geom_histogram(alpha=0.5, col="grey20") +
scale_x_continuous(n.breaks = 10) +
xlab("number of kinases") + ylab("count") +
xlim(0,100) + ylim(0,50) +
ggtitle("Distribution of number \nof kinase targets per drug") +
theme_customScale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.Drug per kinases
plotTab <- tarList %>% filter(`Target Classification` =="High confidence") %>%
group_by(`Gene Name`) %>% summarise(nDrug = length(Drug))
p2 <- ggplot(plotTab, aes(x=nDrug)) + geom_histogram(alpha=0.5, col="grey20") +
scale_x_continuous(n.breaks = 10) +
xlab("number of drugs") + ylab("count") +
xlim(0,100) + ylim(0,70) +
ggtitle("Distribution of number of \ndrugs per kinase target") +
theme_customScale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.Combine for Figure1
cowplot::plot_grid(p1,NULL, p2, rel_widths = c(1,0.1,1), ncol=3)`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.Warning: Removed 5 rows containing non-finite values (stat_bin).Warning: Removed 2 rows containing missing values (geom_bar).`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.Warning: Removed 2 rows containing missing values (geom_bar).
#ggsave("test.pdf", height = 5, width = 12)Save kinobeads data
saveRDS(tarList, file = "../output/allTargets.rds")
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[5] readr_2.1.1 tidyr_1.1.4 tibble_3.1.6 ggplot2_3.3.5
[9] tidyverse_1.3.1 readxl_1.3.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 lubridate_1.8.0 assertthat_0.2.1 rprojroot_2.0.2
[5] digest_0.6.29 utf8_1.2.2 R6_2.5.1 cellranger_1.1.0
[9] backports_1.4.1 reprex_2.0.1 evaluate_0.14 highr_0.9
[13] httr_1.4.2 pillar_1.6.4 rlang_0.4.12 rstudioapi_0.13
[17] jquerylib_0.1.4 rmarkdown_2.11 labeling_0.4.2 munsell_0.5.0
[21] broom_0.7.10 compiler_4.1.2 httpuv_1.6.4 modelr_0.1.8
[25] xfun_0.29 pkgconfig_2.0.3 htmltools_0.5.2 tidyselect_1.1.1
[29] workflowr_1.7.0 fansi_0.5.0 crayon_1.4.2 tzdb_0.2.0
[33] dbplyr_2.1.1 withr_2.4.3 later_1.3.0 grid_4.1.2
[37] jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2
[41] git2r_0.29.0 magrittr_2.0.1 scales_1.1.1 cli_3.1.0
[45] stringi_1.7.6 farver_2.1.0 fs_1.5.2 promises_1.2.0.1
[49] xml2_1.3.3 bslib_0.3.1 ellipsis_0.3.2 generics_0.1.1
[53] vctrs_0.3.8 cowplot_1.1.1 tools_4.1.2 glue_1.6.0
[57] hms_1.1.1 fastmap_1.1.0 yaml_2.2.1 colorspace_2.0-2
[61] rvest_1.0.2 knitr_1.37 haven_2.4.3 sass_0.4.0