Description Usage Arguments Value Examples
An important step to annotate factors is to visualise the corresponding feature weights.
This function plots all weights for a given latent factor and view, labeling the top ones.
In contrast, the function plot_top_weights
displays only the top features with highest loading.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 
object 
a 
view 
a string with the view name, or an integer with the index of the view. 
factors 
character vector with the factor name(s), or numeric vector with the index of the factor(s). 
nfeatures 
number of top features to label. 
color_by 
specifies groups or values (either discrete or continuous) used to color the dots (features). This can be either:

shape_by 
specifies groups or values (only discrete) used to shape the dots (features). This can be either:

abs 
logical indicating whether to take the absolute value of the weights. 
manual 
A nested list of character vectors with features to be manually labelled (see the example for details). 
color_manual 
a character vector with colors, one for each element of 'manual' 
scale 
logical indicating whether to scale all weights from 1 to 1 (or from 0 to 1 if abs=TRUE). 
dot_size 
numeric indicating the dot size. 
text_size 
numeric indicating the text size. 
legend 
logical indicating whether to add legend. 
return_data 
logical indicating whether to return the data frame to plot instead of plotting 
A ggplot
object or a data.frame
if return_data is TRUE
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15  # Using an existing trained model on simulated data
file < system.file("extdata", "model.hdf5", package = "MOFA2")
model < load_model(file)
# Plot distribution of weights for Factor 1 and View 1
plot_weights(model, view = 1, factors = 1)
# Plot distribution of weights for Factors 1 to 3 and View 1
plot_weights(model, view = 1, factors = 1:3)
# Take the absolute value and highlight the top 10 features
plot_weights(model, view = 1, factors = 1, nfeatures = 10, abs = TRUE)
# Change size of dots and text
plot_weights(model, view = 1, factors = 1, text_size = 5, dot_size = 1)

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