Heatmap

infection.total <- read.delim("C:/Users/User/Desktop/HeatMap/Total/1_GO_BP_INFECTION_558entries.txt")
mock.total <- read.delim("C:/Users/User/Desktop/HeatMap/Total/1_GO_BP_MOCK_669entries.txt")

library(tidyverse)
library(lubridate)

## Separando coluna nas dataframes
infection.total.final <- cbind(infection.total$Term, infection.total$PValue, infection.total$Count, infection.total$Fold.Enrichment)
colnames(infection.total.final) <- c("Term", "pvalue_infec", "Count", "Fold Enrichment")
as.data.frame(infection.total.final) -> infection.total.final
infection.total.final %>%
  filter(pvalue_infec <= 0.05) -> infection.total.final
View(infection.total.final)

mock.total.final <- cbind(mock.total$Term, mock.total$PValue, mock.total$Count, mock.total$Fold.Enrichment)
colnames(mock.total.final) <- c("Term", "pvalue_mock", "Count", "Fold Enrichment")
as.data.frame(mock.total.final) -> mock.total.final
mock.total.final %>%
  filter(pvalue_mock <= 0.05) -> mock.total.final
View(mock.total.final)


## Filtrando e juntando dataframes
merge(infection.total.final, mock.total.final, by = "Term") -> final.total 
View(final.total)

write.csv(infection.total.final, "C:/Users/User/BP_infec")

## Ajustando dados na coluna Term 

library(stringr)

term <- final.total$Term
str_remove(term, "[mmu0123456789:]") -> term
str_remove(term, "G") -> term
str_to_title(term) -> term
final.total <- cbind(term, final.total$pvalue_mock, final.total$pvalue_infec)
colnames(final.total) <- c("Term", "pvalue_mock", "pvalue_infec")
View(final.total)

## Impedindo inclusões de NAs
library("gsubfn")
final.total <- as.data.frame(final.total)
final.total$pvalue_infec -> pvalue_infec
final.total$pvalue_mock -> pvalue_mock
gsub(",",".", pvalue_infec) -> pvalue_infec
gsub(",",".", pvalue_mock) -> pvalue_mock
View(final.total)

## Transformando pvalue em numeric 
as.numeric(pvalue_infec) -> p_infec
as.numeric(pvalue_mock) -> p_mock

## Gerando Z-Score
qnorm(p_infec) -> Infection 
qnorm(p_mock) -> Mock 


## Transformando pvalue em log10
-1*log(p_infec) -> Infection 
-1*log(p_mock) -> Mock

## Juntando dados novamente 
data.frame(final.total$Term, Infection, Mock) -> hm_data
View(hm_data)

## Convertendo coluna em row name 
# Usando pacote textshape e função column_to_row_names
library(textshape)
column_to_rownames(hm_data) -> hm_data
View(hm_data)

## Plotando gráfico usando CompleHeatMap pacjage

library(ComplexHeatmap)
library(circlize)

col_fun = colorRamp2(c(-1,-4), c("white", "orange"))
ht1 = Heatmap(as.matrix(hm_data), show_column_dend = F, show_row_dend = F,
              heatmap_legend_param = list(title = "Z Score",
                                          legend_height = unit(3, "cm"),
                                          title_position = "leftcenter-rot"),
              row_names_gp = gpar(fontsize=10),
              width = unit(2, "cm"),
              height = unit(6, "cm"),
              row_names_max_width = unit(7, "cm"),
              column_order = sort(colnames(Infection)),
              col = col_fun
)

draw(ht1, heatmap_legend_side = "left")

dev.off()