diff --git a/heatmaps/h1_simple.R b/heatmaps/h1_simple.R index ea27c43..18f195c 100644 --- a/heatmaps/h1_simple.R +++ b/heatmaps/h1_simple.R @@ -8,7 +8,7 @@ library(RColorBrewer) data <- read.csv("dataset.csv", comment.char="#") rnames <- data[,1] # assign labels in column 1 to "rnames" mat_data <- data.matrix(data[,2:ncol(data)]) # transform column 2-5 into a matrix -rownames(mat_data) <- rnames # assign row names +rownames(mat_data) <- rnames # assign row names @@ -20,27 +20,44 @@ rownames(mat_data) <- rnames # assign row names my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299) # (optional) defines the color breaks manually for a "skewed" color transition -col_breaks = c(seq(-1,0,length=100), # for red - seq(0,0.7,length=100), # for yellow - seq(0.7,1,length=100)) # for green +col_breaks = c(seq(-1,0,length=100), # for red + seq(0.01,0.7,length=100), # for yellow + seq(0.71,1,length=100)) # for green # creates a 5 x 5 inch image -png("h1_simple.png", +png("h1_simple.png", width = 5*300, # 5 x 300 pixels height = 5*300, res = 300, # 300 pixels per inch pointsize = 8) # smaller font size -heatmap.2(mat_data, +heatmap.2(mat_data, cellnote = mat_data, # same data set for cell labels main = "Correlation", # heat map title notecol="black", # change font color of cell labels to black density.info="none", # turns off density plot inside color legend trace="none", # turns off trace lines inside the heat map margins =c(12,9), # widens margins around plot - col=my_palette, # use on color palette defined earlier + col=my_palette, # use on color palette defined earlier breaks=col_breaks, # enable color transition at specified limits dendrogram="row", # only draw a row dendrogram Colv="NA") # turn off column clustering +############################################################################## +# NOTE +############################################################################## +# The color breaks above will yield a warning +# "...unsorted 'breaks' will be sorted before use" since they contain +# (due to the negative numbers). To avoid this warning, you can change the +# manual breaks to: +# +# col_breaks = c(seq(0,1,length=100), # for red +# seq(1.01,1.7,length=100), # for yellow +# seq(1.71,2,length=100)) # for green +# +# However, the problem is then that our heatmap contains negative values +# which will then not be colored correctly. Remember that you don't need to +# provide manual color breaks at all, this is entirely optional. +############################################################################## + dev.off() diff --git a/heatmaps/h1_simple.png b/heatmaps/h1_simple.png index fec6168..95604c7 100644 Binary files a/heatmaps/h1_simple.png and b/heatmaps/h1_simple.png differ diff --git a/heatmaps/h2_default_clustering.R b/heatmaps/h2_default_clustering.R index b405f68..e4ada5b 100644 --- a/heatmaps/h2_default_clustering.R +++ b/heatmaps/h2_default_clustering.R @@ -8,7 +8,7 @@ library(RColorBrewer) data <- read.csv("dataset.csv", comment.char="#") rnames <- data[,1] # assign labels in column 1 to "rnames" mat_data <- data.matrix(data[,2:ncol(data)]) # transform column 2-5 into a matrix -rownames(mat_data) <- rnames # assign row names +rownames(mat_data) <- rnames # assign row names @@ -19,13 +19,8 @@ rownames(mat_data) <- rnames # assign row names # creates a own color palette from red to green my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299) -# (optional) defines the color breaks manually for a "skewed" color transition -col_breaks = c(seq(-1,0,length=100), # for red - seq(0,0.7,length=100), # for yellow - seq(0.7,1,length=100)) # for green - # creates a 5 x 5 inch image -png("h2_default_clustering.png", +png("h2_default_clustering.png", width = 5*300, # 5 x 300 pixels height = 5*300, res = 300, # 300 pixels per inch @@ -37,19 +32,19 @@ png("h2_default_clustering.png", # Distance options: euclidean (default), maximum, canberra, binary, minkowski, manhattan # Cluster options: complete (default), single, average, mcquitty, median, centroid, ward row_distance = dist(mat_data, method = "manhattan") -row_cluster = hclust(row_distance, method = "ward") +row_cluster = hclust(row_distance, method = "ward.D") col_distance = dist(t(mat_data), method = "manhattan") -col_cluster = hclust(col_distance, method = "ward") +col_cluster = hclust(col_distance, method = "ward.D") -heatmap.2(mat_data, +heatmap.2(mat_data, cellnote = mat_data, # same data set for cell labels main = "Correlation", # heat map title notecol = "black", # change font color of cell labels to black# density.info = "none", # turns off density plot inside color legend trace = "none", # turns off trace lines inside the heat map margins = c(12,9), # widens margins around plot - col = my_palette, # use on color palette defined earlier - breaks = col_breaks, # enable color transition at specified limits + col = my_palette, # use on color palette defined earlier Rowv = as.dendrogram(row_cluster), # apply default clustering method Colv = as.dendrogram(col_cluster)) # apply default clustering method + dev.off() diff --git a/heatmaps/h2_default_clustering.png b/heatmaps/h2_default_clustering.png index e6cddf6..2d9c73f 100644 Binary files a/heatmaps/h2_default_clustering.png and b/heatmaps/h2_default_clustering.png differ diff --git a/heatmaps/h3_categorizing.R b/heatmaps/h3_categorizing.R index 89afb51..9c6517d 100644 --- a/heatmaps/h3_categorizing.R +++ b/heatmaps/h3_categorizing.R @@ -8,7 +8,7 @@ library(RColorBrewer) data <- read.csv("dataset.csv", comment.char="#") rnames <- data[,1] # assign labels in column 1 to "rnames" mat_data <- data.matrix(data[,2:ncol(data)]) # transform column 2-5 into a matrix -rownames(mat_data) <- rnames # assign row names +rownames(mat_data) <- rnames # assign row names @@ -19,19 +19,14 @@ rownames(mat_data) <- rnames # assign row names # creates a own color palette from red to green my_palette <- colorRampPalette(c("red", "yellow", "green"))(n = 299) -# (optional) defines the color breaks manually for a "skewed" color transition -col_breaks = c(seq(-1,0,length=100), # for red - seq(0,0.7,length=100), # for yellow - seq(0.7,1,length=100)) # for green - # creates a 5 x 5 inch image -png("h3_categorizing.png", +png("h3_categorizing.png", width = 5*300, # 5 x 300 pixels height = 5*300, res = 300, # 300 pixels per inch pointsize = 8) # smaller font size -heatmap.2(mat_data, +heatmap.2(mat_data, cellnote = mat_data, # same data set for cell labels RowSideColors = c( # grouping row-variables into different rep("gray", 3), # categories, Measurement 1-3: green @@ -43,7 +38,6 @@ heatmap.2(mat_data, trace="none", # turns off trace lines inside the heat map margins =c(12,9), # widens margins around plot col=my_palette, # use on color palette defined earlier - breaks=col_breaks, # enable color transition at specified limits dendrogram="row", # only draw a row dendrogram Colv="NA") # turn off column clustering @@ -54,6 +48,6 @@ legend("topright", # location of the legend on the heatmap plot col = c("gray", "blue", "black"), # color key lty = 1, # line style lwd = 10, # line width - ) + ) dev.off() diff --git a/heatmaps/h3_categorizing.png b/heatmaps/h3_categorizing.png index 4c67517..9cfc95a 100644 Binary files a/heatmaps/h3_categorizing.png and b/heatmaps/h3_categorizing.png differ