5_tables.Rmd

---
output:
  html_document: default
  pdf_document: default
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, cache = TRUE)
```

## Libraries and folders

```{r}
library(dplyr)

dir.create("tables", showWarnings = FALSE)
```

## Table S1

```{r}
s1 <- read.delim("results/S_cerevisiae/DESeq2/S_cerevisiae_merged_salt_lfc1_p05_results.tsv", stringsAsFactors = FALSE)

# Select columns and create stressType column
s1 <- s1 %>% select(ensembl_gene_id, external_gene_name, log2FoldChange, lfcSE, padj) %>%
  mutate(stressType = ifelse(test = log2FoldChange >= 1 & padj <= 0.05, 
                             yes = "upregulated", no = ifelse(test = log2FoldChange <=- 1 & padj <= 0.05, 
                                                              yes = "downregulated", no = "unresponsive")))

write.table(x = s1, file = "tables/Supplementary_Table_1_OsmoAtlas.tab", quote = FALSE, sep = "\t", row.names = FALSE)
```


## Table S2

```{r}
s2 <- read.delim("results/S_cerevisiae/stressConsensus_Properties_Full_Table.tsv", stringsAsFactors = FALSE)

colnames(s2)[3:4] <- c("stressType", "hog1Dependency")

write.table(x = s2, file = "tables/Supplementary_Table_2_Yeast_StressFeatures.tab", row.names = FALSE, quote = FALSE, sep = "\t")
```


## Table S3

```{r}
s3 <- read.delim("results/S_cerevisiae/medianValues_features_stressGroups.tab", stringsAsFactors = FALSE)

write.table(x = s3, file = "tables/Supplementary_Table_3_Yeast_MedianValues_Wilcoxon.tab", row.names = FALSE, quote = FALSE, sep = "\t")
```

## Table S4

Table copied directly from HOMER results


## Table S5

```{r}
s5 <- read.delim("data/original_data/Cate_DESeq2_salt_vs_nostress.tsv", stringsAsFactors = FALSE)

colnames(s5)[1:2] <- c("ensembl_gene_id", "external_gene_name")
# Select columns and create stressType column
s5 <- s5 %>% select(ensembl_gene_id, external_gene_name, log2FoldChange, lfcSE, padj) %>%
  mutate(stressType = ifelse(test = log2FoldChange >= 1 & padj <= 0.05, 
                             yes = "upregulated", no = ifelse(test = log2FoldChange <=- 1 & padj <= 0.05, 
                                                              yes = "downregulated", no = "unresponsive")))

write.table(x = s5, file = "tables/Supplementary_Table_5_HeLa_osmostressResponsive.tab", quote = FALSE, sep = "\t", row.names = FALSE)
```

## Table S6

```{r}
s6 <- read.delim("results/human/humanStressConsensus_Properties_Full_Table.tsv", stringsAsFactors = FALSE)

colnames(s6)[3] <- "stressType_HeLa"

write.table(x = s6, file = "tables/Supplementary_Table_6_Human_StressFeatures.tab", row.names = FALSE, quote = FALSE, sep ="\t")
```

## Table S7

```{r}
s7 <- read.delim("results/human/medianValues_features_human_stressGroups.tab", stringsAsFactors = FALSE)
write.table(x = s7, file = "tables/Supplementary_Table_7_Human_MedianValues_Wilcoxon.tab", row.names = FALSE, quote = FALSE, sep = "\t")

```