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supplementary_tables.Rmd
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supplementary_tables.Rmd
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---
title: "Code to generate supplementary tables"
output:
html_document:
keep_md: yes
toc: yes
theme: united
code_folding: hide
editor_options:
chunk_output_type: console
---
# General settings
```{r setup}
knitr::opts_chunk$set(
echo = TRUE,
warning = FALSE,
message = FALSE,
include = TRUE,
cache = TRUE,
cache.lazy = FALSE,
eval = TRUE,
fig.width = 4 * (1 + sqrt(5)) / 2,
fig.height = 4,
dpi = 700
)
knitr::opts_knit$set(root.dir = "~/Documents/01_repos/kidney_fibrosis/")
```
## Packages
```{r, message=F, warning =F, include=}
library(tidyverse)
library(ggplot2);theme_set(cowplot::theme_cowplot(font_size = 15) + theme(panel.grid.major = element_line(colour = "lightgrey", linewidth = 0.2), panel.grid.minor = element_line(colour = "lightgrey", linewidth = 0.2)))
library("reshape2")
library(ggrepel)
library(knitr)
library(Biostrings)
library(RColorBrewer)
library(visNetwork)
mutate <- dplyr::mutate
select <- dplyr::select
group_by <- dplyr::group_by
```
```{r}
load("data/processed_data/2024-08-15_diff_results.RData")
load("results/2024-07-24_tf_enrichment_results.RData")
load("results/2024-07-24_kinase_enrichment_result.RData")
load("results/2024-09-02_pathwayenrichment_results.RData")
load("results/2024-08-16_res_network.RData")
```
```{r}
supplementary_tables <- list(
"explanation" = readxl::read_excel(here::here("suppdata_firstpage.xlsx"), sheet = 1),
"S1_DEresults" = diff_results %>% select(modality, feature_id, time, logFC, adj.P.Val),
"S2_pathwayenrichment" = decoupler_results %>% filter(statistic == "norm_wmean" & p_value < 0.05 & abs(score) > 1.7),
"S3_enzyme_enrichment" = bind_rows("Kinase/phosphatase" = res_kinase_enrichment$enrichment %>% filter(statistic == "mnorm_wmean" & p_value < 0.03 & abs(score) > 3), "Transcription factor" = res_tf_enrichment$enrichment %>% filter(p_value < 0.03 & abs(score) > 3), .id= "enzyme_type") %>% select(enzyme_type, source, time, score, p_value),
"S4_network_edgetable" = res_network$combined_edges_df,
"S5_network_nodetable" =res_network$node_df,
"S6_qPCRprimers" = readxl::read_excel(here::here("supptables_manualpart.xlsx"), sheet = 1),
"S7_siRNA_sequences" = readxl::read_excel(here::here("supptables_manualpart.xlsx"), sheet = 2),
"S8_initial_imaging" = read.csv("data/NT22_004_Col1_20240127.csv"),
"S9_imaging_validation" = read.csv("data/NT24_001_CNA35_20240224.csv"),
"S10_qPCR_data" = read.csv("results/2024-09-19_combined_qPCR_datatable.csv")
)
supplementary_tables <- lapply(supplementary_tables, as.data.frame)
openxlsx::write.xlsx(supplementary_tables, file = here::here("Supplementary_Data.xlsx"))
```
```{r}
```