While writing new examples for the SSM vignette, I discovered that the classification_column parameter does not work as advertised for this function. Or more specifically, this line in the function does not do what it is supposed to do:
I am assuming that the goal here is to create a new column in the meta_arranged df called classification, that will be used by the colour parameter inside the ggplot argument later on. This code instead creates a new column filled with NAs (looking for a factor with the same name as the value for classification_column?) Resulting in the following plot (no colouring based on the selected classification column):
The example plot here was generated with the following code:
In addition, it would be nice to have the function automatically subset the colours in the retrieved palette to the factors in the classification_column (FL and DLBCL, pathology).
While writing new examples for the SSM vignette, I discovered that the
classification_column
parameter does not work as advertised for this function. Or more specifically, this line in the function does not do what it is supposed to do:meta_arranged$classification = factor(meta_arranged[,classification_column], levels = unique(meta_arranged[,classification_column]))
I am assuming that the goal here is to create a new column in the meta_arranged df called classification, that will be used by the
colour
parameter inside the ggplot argument later on. This code instead creates a new column filled with NAs (looking for a factor with the same name as the value for classification_column?) Resulting in the following plot (no colouring based on the selected classification column):The example plot here was generated with the following code:
In addition, it would be nice to have the function automatically subset the colours in the retrieved palette to the factors in the classification_column (FL and DLBCL, pathology).