Btukfyl

I am trying to create a heatmap using Heatmap in Rstudio.

My data file is tab separated text file, with a header row (row names in Heatmap), and the 1st and 2nd column indicate my heatmap column names (I want those to show as columns labels in my heatmap)

Here is my script:

filename <- "Heatmapii.csv"

my_data <- read.table(filename, sep=",", header = TRUE)



#Transform data into a matrix)

my_matrix <- as.matrix(my_data[ ,c(3:23)]) # leave out the first 2 columns 



# Save Time column for annotating the heatmap later (1st column)

time_info <- data.frame(time=my_data$Time) 



# Save Treatment column for annotating the heatmap later (2nd column)

treatment_info <- data.frame(treatment=my_data$Treatment) 



Heatmap(my_matrix) 



# Flip rows and columns around

my_matrix <- t(my_matrix)

Heatmap(my_matrix)



colnames(my_matrix) <- my_data$Time



# Create heatmap by showing 1st column names

Heatmap(my_matrix, 

    show_column_names = TRUE,

    cluster_rows =FALSE, 

    cluster_columns = FALSE,

    row_names_side = "left")



# Assign different colors for 2nd column of my_data

treatment.colors <- c("grey","lightblue")



# set the names for treatment.columns

names(treatment.colors) <- paste(c("Control","Inoculated"), sep = "")



Heatmap(my_matrix, 

    show_column_names = TRUE,

    cluster_rows =FALSE, 

    cluster_columns = FALSE,

    row_names_side = "left",

    bottom_annotation = HeatmapAnnotation

    (treatment_info, col = list(treatment=treatment.colors), 

    show_legend = TRUE)

So, basically I managed to add the second column on the x-axis only as different colours. I would like to maybe keep the different colours, but to also demonstrate the names that correspond to these colours on the heatmap.

I am very new to R, so could you please help me with that?