library(openxlsx)
a <- loadWorkbook('Dxterity2/Dxterity4.xlsx')
sheetNames <- sheets(a)
a11<- read.xlsx('Dxterity2/Dxterity4.xlsx', sheet=2)
a11[1:5,1:5]
dim(a11)
colnames(a11)
rownames(a11)
which(colnames(a11)=="Timepoint")
### 7 to 40
row_hc<- which(a11[,5]=="HC")
row_A<- which(a11[,5]=="A" & a11[,4]=="SLE")
length(row_A)
data_hc<- a11[c(row_hc),
              c(10:43)]
updated_col<- c(25,27,28,31,23,33,34,14,15,16,18,3,4,17,20,32,30)
data_hc1<- data_hc[,updated_col]
colnames(data_hc1)
data_SLEA<- a11[c(row_A),
                c(10:43)]
updated_col<- c(25,27,28,31,23,33,34,14,15,16,18,3,4,17,20,32,30)
data_SLEA1<- data_SLEA[,updated_col]
rslea<- a11$Client.Specimen.ID[as.numeric(rownames(data_SLEA1))]
#rownames(data_SLEA1)<- rslea
rhc<- a11$Client.Specimen.ID[as.numeric(rownames(data_hc1))]
rownames(data_hc1)<- rhc
.rowNamesDF(data_hc1, make.names=T) <- rhc
.rowNamesDF(data_SLEA1, make.names=T) <- rslea

cor_hc<- cor(data_hc1,method = "pearson")
cor_SLEA<- cor(data_SLEA1,method = "pearson")
###########################################################

library(grid)
library(ggplotify)

markerhccvid<- rbind(data_hc1,data_SLEA1)

markerhccvid1<- markerhccvid

library(pheatmap)
library(RColorBrewer)
library(viridis)

mat_breaks <- seq(min(markerhccvid1), max(markerhccvid1), length.out = 90)
p<- pheatmap(
  mat               = markerhccvid1,
  color             = inferno(length(mat_breaks) - 1),
  breaks            = mat_breaks,
  border_color      = NA,
  show_colnames     = TRUE,
  show_rownames     = TRUE,
  #annotation_col    = mat_col,
  #annotation_colors = mat_colors,
  drop_levels       = TRUE,
  fontsize          = 14,
  main              = "Heatmap of HC and SLE at Timepoint A"
)


pdf("Dxterity2/heatmap_hc_SLEA.pdf", 7, 8)
p
dev.off()

########################################


mat_breaks <- seq(-1, 1, length.out = 90)
p1<- pheatmap(
  mat               = cor_hc,
  color             = inferno(length(mat_breaks) - 1),
  breaks            = mat_breaks,
  border_color      = NA,
  show_colnames     = TRUE,
  show_rownames     = TRUE,
  #annotation_col    = mat_col,
  #annotation_colors = mat_colors,
  drop_levels       = TRUE,
  fontsize          = 14,
  main              = "Correlation heatmap of HC"
)


pdf("Dxterity2/corr_heatmap_hc.pdf", 7, 8)
p1
dev.off()


#####  cluster_rows=FALSE, cluster_cols=FALSE

mat_breaks <- seq(-1, 1, length.out = 90)
p11<- pheatmap(
  mat               = cor_hc,
  color             = inferno(length(mat_breaks) - 1),
  breaks            = mat_breaks,
  border_color      = NA,
  show_colnames     = TRUE,
  show_rownames     = TRUE,
  #annotation_col    = mat_col,
  #annotation_colors = mat_colors,
  drop_levels       = TRUE,
  fontsize          = 14,cluster_rows=FALSE, cluster_cols=FALSE,
  main              = "Ordered correlation heatmap of HC",
  
)


pdf("Dxterity2/ordered_corr_heatmap_hc.pdf", 7, 8)
p11
dev.off()


############################################################################

########################################


mat_breaks <- seq(-1, 1, length.out = 90)
p2<- pheatmap(
  mat               = cor_SLEA,
  color             = inferno(length(mat_breaks) - 1),
  breaks            = mat_breaks,
  border_color      = NA,
  show_colnames     = TRUE,
  show_rownames     = TRUE,
  #annotation_col    = mat_col,
  #annotation_colors = mat_colors,
  drop_levels       = TRUE,
  fontsize          = 14,
  main              = "Correlation heatmap of SLE at timepoint A"
)


pdf("Dxterity2/corr_heatmap_SLEA.pdf", 7, 8)
p2
dev.off()


#####  cluster_rows=FALSE, cluster_cols=FALSE

mat_breaks <- seq(-1, 1, length.out = 90)
p21<- pheatmap(
  mat               = cor_SLEA,
  color             = inferno(length(mat_breaks) - 1),
  breaks            = mat_breaks,
  border_color      = NA,
  show_colnames     = TRUE,
  show_rownames     = TRUE,
  #annotation_col    = mat_col,
  #annotation_colors = mat_colors,
  drop_levels       = TRUE,
  fontsize          = 14,cluster_rows=FALSE, cluster_cols=FALSE,
  main              = "Ordered correlation heatmap of SLE at timepoint A",
  
)


pdf("Dxterity2/ordered_corr_heatmap_SLEA.pdf", 7, 8)
p21
dev.off()