how to add second x-axis labels (annotations) in Heatmap (Bioconductor)
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$Time
# Create heatmap by showing 1st column names
Heatmap(my_matrix,
show_column_names = TRUE,
cluster_rows =FALSE,
cluster_columns = FALSE,
row_names_side = "left")
# Assign different colors for 2nd column of my_data
treatment.colors <- c("grey","lightblue")
# set the names for treatment.columns
names(treatment.colors) <- paste(c("Control","Inoculated"), sep = "")
Heatmap(my_matrix,
show_column_names = TRUE,
cluster_rows =FALSE,
cluster_columns = FALSE,
row_names_side = "left",
bottom_annotation = HeatmapAnnotation
(treatment_info, col = list(treatment=treatment.colors),
show_legend = TRUE)
So, basically I managed to add the second column on the x-axis only as different colours. I would like to maybe keep the different colours, but to also demonstrate the names that correspond to these colours on the heatmap.
I am very new to R, so could you please help me with that?
r rstudio legend heatmap
asked Nov 21 '18 at 16:29
Vassen
11
add a comment |
I am trying to create a heatmap using Heatmap in Rstudio.
My data file is tab separated text file, with a header row (row names in Heatmap), and the 1st and 2nd column indicate my heatmap column names (I want those to show as columns labels in my heatmap)
Here is my script:
filename <- "Heatmapii.csv"
my_data <- read.table(filename, sep=",", header = TRUE)
#Transform data into a matrix)
my_matrix <- as.matrix(my_data[ ,c(3:23)]) # leave out the first 2 columns
# Save Time column for annotating the heatmap later (1st column)
time_info <- data.frame(time=my_data$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?
r rstudio legend heatmap
asked Nov 21 '18 at 16:29
Vassen
11
add a comment |
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$Time
# Create heatmap by showing 1st column names
Heatmap(my_matrix,
show_column_names = TRUE,
cluster_rows =FALSE,
cluster_columns = FALSE,
row_names_side = "left")
# Assign different colors for 2nd column of my_data
treatment.colors <- c("grey","lightblue")
# set the names for treatment.columns
names(treatment.colors) <- paste(c("Control","Inoculated"), sep = "")
Heatmap(my_matrix,
show_column_names = TRUE,
cluster_rows =FALSE,
cluster_columns = FALSE,
row_names_side = "left",
bottom_annotation = HeatmapAnnotation
(treatment_info, col = list(treatment=treatment.colors),
show_legend = TRUE)
So, basically I managed to add the second column on the x-axis only as different colours. I would like to maybe keep the different colours, but to also demonstrate the names that correspond to these colours on the heatmap.
I am very new to R, so could you please help me with that?
r rstudio legend heatmap
asked Nov 21 '18 at 16:29
Vassen
11
I am trying to create a heatmap using Heatmap in Rstudio.
My data file is tab separated text file, with a header row (row names in Heatmap), and the 1st and 2nd column indicate my heatmap column names (I want those to show as columns labels in my heatmap)
Here is my script:
filename <- "Heatmapii.csv"
my_data <- read.table(filename, sep=",", header = TRUE)
#Transform data into a matrix)
my_matrix <- as.matrix(my_data[ ,c(3:23)]) # leave out the first 2 columns
# Save Time column for annotating the heatmap later (1st column)
time_info <- data.frame(time=my_data$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?
r rstudio legend heatmap
r rstudio legend heatmap
asked Nov 21 '18 at 16:29
Vassen
11
asked Nov 21 '18 at 16:29
Vassen
11
asked Nov 21 '18 at 16:29
Vassen
11
asked Nov 21 '18 at 16:29
Vassen
11
asked Nov 21 '18 at 16:29
Vassen
11
11
add a comment |
add a comment |
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