This is the figure Im getting what I would like to get is only the density instead of the scatter, how do i get that this ?
The function that is used here is part of the MOFA2 package I tried tinkering around the source code by charging the dot_size parameter to 0
but no effect.
The actual code which I used to plot this
plot_factors(MOFAobject,
factors = 1:3,
color_by = "RISK_CYTO"
)
Any suggestion or help would be really appreciated
Data update MOFA
dt = fread("ftp://ftp.ebi.ac.uk/pub/databases/mofa/getting_started/data.txt.gz")
head(dt)
dt[,group:=NULL]
MOFAobject <- create_mofa(dt)
print(MOFAobject)
data_opts <- get_default_data_options(MOFAobject)
head(data_opts)
model_opts <- get_default_model_options(MOFAobject)
head(model_opts)
train_opts <- get_default_training_options(MOFAobject)
head(train_opts)
MOFAobject <- prepare_mofa(
object = MOFAobject,
data_options = data_opts,
model_options = model_opts,
training_options = train_opts
)
Train the MOFA model
outfile = file.path(getwd(),"model.hdf5")
MOFAobject.trained <- run_mofa(MOFAobject, outfile)
Plot factors
plot_factors(MOFAobject,
factors = 1:3,
color_by = "group"
)