Cytobands.Rmd

---
title: "Cytobands"
author: "Alicia Pliego"
output: 
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    toc_float: true
    toc_collapsed: true
    toc_depth: 3
    number_sections: true
    theme: sandstone
---
<style>
body {
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# Gene Level copy number file from TCGA

Downloading the Gene level Copy number files from TCGA, I computed CIN in the following way:
  - gene CNV > 2.25 = Amp
  - gene CNV < 1.75 = Del 
```{r , echo=FALSE, warning=FALSE, message=FALSE}
library(chromoMap)
library(tidyverse)
library(heatmaply)
library(org.Hs.eg.db)
library(dplyr)
library(Matrix)
library(data.table)
```

```{r , echo=FALSE, warning=FALSE, message=FALSE}
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
x <- as.list(org.Hs.egMAP)
# Get the entrez gene identifiers that are mapped to any cytoband
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])

```

```{r , echo=FALSE, warning=FALSE, message=FALSE}
# chromosome files
list_gene_names <- read.table("gene_level/gene_level_template.tsv",sep = "\t", header = TRUE)
```

```{r , echo=FALSE, warning=FALSE, message=FALSE}
list_gene_names$entrez <- mapIds(org.Hs.eg.db,
                            keys=list_gene_names$gene_name,
                            column="ENTREZID",
                            keytype="SYMBOL",
                            multiVals="first")
list_gene_names <- na.omit(list_gene_names)
```

```{r , echo=FALSE, warning=FALSE, message=FALSE}
list_gene_names_cyto <- xx[list_gene_names$entrez]
# Mapping -> converting the list to 
# dataframe
list_gene_names_cyto <- t(sapply(list_gene_names_cyto,c))
list_gene_names_cyto <- t(list_gene_names_cyto)
#write.table(list_gene_names_cyto, "gene_level/cytoband_anno.tsv",sep = "\t", quote = FALSE)
list_gene_names_cyto_df <- read.table("gene_level/cytoband_anno.tsv", header = TRUE)

```

```{r , echo=FALSE, warning=FALSE, message=FALSE}
#list_gene_names_cyto_df$symbol <- mapIds(org.Hs.eg.db,
#                            keys=list_gene_names_cyto_df$entrez,
#                            column="SYMBOL",
#                            keytype="ENTREZID",
#                            multiVals="first")
list_gene_names_cyto_df <- na.omit(list_gene_names_cyto_df)
list_gene_names_cyto_df <- as.data.frame(list_gene_names_cyto_df)
#write.table(list_gene_names_cyto_df, "gene_level/cytoband_anno.tsv",sep = "\t", quote = FALSE)
```

I have mapped cytobands to gene entrez ids using org.Hs.egMAP and using the cytobands I extract the gene level CIN which will be added at cytoband level for all the genes in that cytoband across all the different cases that we have from TCGA-SARC

Plots:
 1- Overall boxplots: for each chromosome all the cytoband CIN per sarcoma type  
 
 1b - Overall heatmap: for each chromosome a heatmap with all the CIN per cytobands and annotation on the side for each sarcoma type  
 
 2- HRD boxplots: The same as before but separating HRDhigh/low  
 
 2b - is there any cytoband differentially expressed between HRD/low groups in particular?  
 3- Make enrichment in those cytobands :)
 

```{r , echo=FALSE, warning=FALSE, message=FALSE}
cyto_chr1 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr1.tsv', sep = '\t', header = TRUE)
cyto_chr2 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr2.tsv', sep = '\t', header = TRUE)
cyto_chr3 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr3.tsv', sep = '\t', header = TRUE)
cyto_chr4 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr4.tsv', sep = '\t', header = TRUE)
cyto_chr5 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr5.tsv', sep = '\t', header = TRUE)
cyto_chr6 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr6.tsv', sep = '\t', header = TRUE)
cyto_chr7 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr7.tsv', sep = '\t', header = TRUE)
cyto_chr8 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr8.tsv', sep = '\t', header = TRUE)
cyto_chr9 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr9.tsv', sep = '\t', header = TRUE)
cyto_chr10 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr10.tsv', sep = '\t', header = TRUE)
cyto_chr11 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr11.tsv', sep = '\t', header = TRUE)
cyto_chr12 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr12.tsv', sep = '\t', header = TRUE)
cyto_chr13 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr13.tsv', sep = '\t', header = TRUE)
cyto_chr14 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr14.tsv', sep = '\t', header = TRUE)
cyto_chr15 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr15.tsv', sep = '\t', header = TRUE)
cyto_chr16 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr16.tsv', sep = '\t', header = TRUE)
cyto_chr17 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr17.tsv', sep = '\t', header = TRUE)
cyto_chr18 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr18.tsv', sep = '\t', header = TRUE)
cyto_chr19 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr19.tsv', sep = '\t', header = TRUE)
cyto_chr20 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr20.tsv', sep = '\t', header = TRUE)
cyto_chr21 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr21.tsv', sep = '\t', header = TRUE)
cyto_chr22 <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr22.tsv', sep = '\t', header = TRUE)
```

```{r , echo=FALSE, warning=FALSE, message=FALSE}
gene_level_anno <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/HRDgenes_gene_level_meta.tsv', sep = '\t', header = TRUE)
row.names(gene_level_anno) <- gene_level_anno$Case_ID
```

## Chromosome 1 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr1) <- cyto_chr1$Case_ID
cyto_chr1$Case_ID <-NULL
cyto_chr1_scaled <-  scale(cyto_chr1)

z_scores_chr1 <- (data-mean(cyto_chr1))/sd(cyto_chr1)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr1_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr1_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr1_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,2000)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr1_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,2000)))
fig

```

## Chromosome 2 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr2) <- cyto_chr2$Case_ID
cyto_chr2$Case_ID <-NULL
cyto_chr2_scaled <-  scale(cyto_chr2)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr2_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr2_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr2_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,2000)))
fig

```


```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr2_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 3 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr3) <- cyto_chr3$Case_ID
cyto_chr3$Case_ID <-NULL
cyto_chr3_scaled <-  scale(cyto_chr3)
```


```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr3_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr3_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr3_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr3_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 4 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr4) <- cyto_chr4$Case_ID
cyto_chr4$Case_ID <-NULL
cyto_chr4_scaled <-  scale(cyto_chr4)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr4_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr4_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr4_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr4_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 5 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr5) <- cyto_chr5$Case_ID
cyto_chr5$Case_ID <-NULL
cyto_chr5_scaled <-  scale(cyto_chr5)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr5_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr5_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr5_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr5_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 6 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr6) <- cyto_chr6$Case_ID
cyto_chr6$Case_ID <-NULL
cyto_chr6_scaled <-  scale(cyto_chr6)
```


```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr6_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr6_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr6_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr6_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 7 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr7) <- cyto_chr7$Case_ID
cyto_chr7$Case_ID <-NULL
cyto_chr7_scaled <-  scale(cyto_chr7)
```


```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr7_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr7_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr7_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr7_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 8 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr8) <- cyto_chr8$Case_ID
cyto_chr8$Case_ID <-NULL
cyto_chr8_scaled <-  scale(cyto_chr8)
```


```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr8_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr8_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr8_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr8_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```


## Chromosome 9 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr9) <- cyto_chr9$Case_ID
cyto_chr9$Case_ID <-NULL
cyto_chr9_scaled <-  scale(cyto_chr9)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr9_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr9_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr9_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr9_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 10 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr10) <- cyto_chr10$Case_ID
cyto_chr10$Case_ID <-NULL
cyto_chr10_scaled <-  scale(cyto_chr10)
```


```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr10_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr10_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr10_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr10_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 11 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr11) <- cyto_chr11$Case_ID
cyto_chr11$Case_ID <-NULL
cyto_chr11_scaled <-  scale(cyto_chr11)
```


```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr11_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr11_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr11_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr11_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 12 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr12) <- cyto_chr12$Case_ID
cyto_chr12$Case_ID <-NULL
cyto_chr12_scaled <-  scale(cyto_chr12)
```


```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr12_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr12_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr12_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr12_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 13 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr13) <- cyto_chr13$Case_ID
cyto_chr13$Case_ID <-NULL
cyto_chr13_scaled <-  scale(cyto_chr13)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr13_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr13_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr13_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr13_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 14 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr14) <- cyto_chr14$Case_ID
cyto_chr14$Case_ID <-NULL
cyto_chr14_scaled <-  scale(cyto_chr14)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr14_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr14_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr14_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr14_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 15 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr15) <- cyto_chr15$Case_ID
cyto_chr15$Case_ID <-NULL
cyto_chr15_scaled <-  scale(cyto_chr15)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr15_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr15_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr15_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr15_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 16 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr16) <- cyto_chr16$Case_ID
cyto_chr16$Case_ID <-NULL
cyto_chr16_scaled <-  scale(cyto_chr16)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr16_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr16_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr16_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr16_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 17 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr17) <- cyto_chr17$Case_ID
cyto_chr17$Case_ID <-NULL
cyto_chr17_scaled <-  scale(cyto_chr17)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr17_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr17_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr17_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr17_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 18 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr18) <- cyto_chr18$Case_ID
cyto_chr18$Case_ID <-NULL
cyto_chr18_scaled <-  scale(cyto_chr18)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr18_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr18_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr18_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr18_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 19 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr19) <- cyto_chr19$Case_ID
cyto_chr19$Case_ID <-NULL
cyto_chr19_scaled <-  scale(cyto_chr19)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr19_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr19_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr19_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr19_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 20 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr20) <- cyto_chr20$Case_ID
cyto_chr20$Case_ID <-NULL
cyto_chr20_scaled <-  scale(cyto_chr20)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr20_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr20_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr20_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr20_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 21 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr21) <- cyto_chr21$Case_ID
cyto_chr21$Case_ID <-NULL
cyto_chr21_scaled <-  scale(cyto_chr21)
```


```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr21_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr21_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr21_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr21_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

## Chromosome 22 Cytobands
```{r , echo=FALSE, warning=FALSE, message=FALSE}
rownames(cyto_chr22) <- cyto_chr22$Case_ID
cyto_chr22$Case_ID <-NULL
cyto_chr22_scaled <-  scale(cyto_chr22)
```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 30, fig.height = 7, fig.align='center'}
cyto_chr22_bp <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/gene_level/cytobands_chr22_bp.tsv', sep = '\t', header = TRUE)

fig <- plot_ly(cyto_chr22_bp,x =~cytoband,  y = ~CN, color = ~Type,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

```{r, echo=FALSE, warning=FALSE, message=FALSE, fig.width= 20, fig.height = 7, fig.align='center'}
fig <- plot_ly(cyto_chr22_bp,x =~cytoband,  y = ~CN, color = ~HRD34,  type = "box",  notched=TRUE) %>%
layout(boxmode = "group",
     yaxis = list(range=c(0,35)))
fig

```

T -test of cytobands in python pval < 0.01

* Chromosome 1:

  - ddLPS 2p11.1 6.978914699947862e-05
  - ddLPS 2p11.2 0.0009328203594964292
  - ddLPS 2q11.1 0.0003306106662498429
  - ddLPS 2q11.2 0.0007483821759446633
  - ddLPS 2q11.2-q12.1 0.0008703008338573793
  - ddLPS 2q12-q14 0.004288188013925764
  - ddLPS 2q12.1 0.0010700572210934063
  - ddLPS 2q12.1-q12.2 0.0015421657073293685
  - ddLPS 2q12.2 0.0010208739707162464
  - ddLPS 2q12.3 0.0010315552453219951
  - ddLPS 2q13 0.0021797548258337828
  - ddLPS 2q13-q14.1 0.004288188013925764
  - ddLPS 2q14.1 0.006122195261664565
  - ddLPS 2q14.1-q14.2 0.0049770919257404525
  - ddLPS 2q21.2 0.009925282742590597
  - LMS 2p11.1 0.0030093585067312214
  - LMS 2q11.1 0.0009351673246347108
  - LMS 2q11.2 0.0010391549785624679
  - LMS 2q14.2-q14.3 0.00864557480824809
  - uLMS 2p14 0.008471017648941986
  - uLMS 2p15 0.003009416227452064
  - uLMS 2p15-p14 0.0072849500425245595
  - uLMS 2p16.1 0.004216181947663537
  - uLMS 2p16.1-p15 0.0037613261075078942
  - uLMS 2q11.1 0.0016958778150337173
  - uLMS 2q11.2 0.006741728286083317
  - uLMS 2q12-q14 0.0031034299247518155
  - uLMS 2q12.2 0.007912738358005785
  - uLMS 2q14.1 0.00422135953924269
  
* Chromosome 2:





## ------------------- ChromoMAP -----------------------##
```{r , echo=FALSE, warning=FALSE, message=FALSE}
# chromosome files
chr_file_1 = read.table("/Users/aliciapliego/Projects/HRDsarcoma/chromoMap/chr_anno.tsv",sep = "\t")

# annotation files
anno_file_1 = read.table("/Users/aliciapliego/Projects/HRDsarcoma/chromoMap/gene_level1.tsv",sep = "\t")
```

```{r , echo=FALSE, warning=FALSE, message=FALSE}

# passing data.frames directly instead of files
chromoMap(list(chr_file_1),list(anno_file_1))
```

```{r , echo=FALSE, warning=FALSE, message=FALSE}
chromoMap("/Users/aliciapliego/Projects/HRDsarcoma/chromoMap/chr_anno.tsv","/Users/aliciapliego/Projects/HRDsarcoma/chromoMap/gene_level1.tsv",
          data_based_color_map = T,
          data_type = "numeric",
          plots = "bar",
          data_colors = list(c("orange","yellow")))
```

  
```{r , echo=FALSE, warning=FALSE, message=FALSE}
cindex_gene_level_cnv <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/data/HRDgenes_all_gene_level.tsv', sep = '\t', header = TRUE)
cindex_gene_level_cnv <- unique(cindex_gene_level_cnv)
rownames(cindex_gene_level_cnv) <- cindex_gene_level_cnv$Case_ID
cindex_gene_level_cnv$Case_ID <- NULL
cindex_gene_level_meta <- read.table('/Users/aliciapliego/Projects/HRDsarcoma/data/HRDgenes_all_gene_level_meta.tsv', sep = '\t', header = TRUE)
cindex_gene_level_meta$X <- NULL
cindex_gene_level_meta <- cindex_gene_level_meta[cindex_gene_level_meta$Case_ID %in% rownames(cindex_gene_level_cnv),]

```

```{r , echo=FALSE, warning=FALSE, message=FALSE}
cindex_gene_level_cnv_t <- t(cindex_gene_level_cnv)
cindex_gene_level_cnv_t$entrez <- mapIds(org.Hs.eg.db,
                            keys=rownames(cindex_gene_level_cnv_t),
                            column="ENSEMBL",
                            keytype="SYMBOL",
                            multiVals="first")
```