plot_factors_vs_cov {MOFA2} | R Documentation |
Scatterplots of a factor's values againt the sample covariates
plot_factors_vs_cov( object, factors = "all", covariates = NULL, warped = TRUE, show_missing = TRUE, scale = FALSE, color_by = NULL, shape_by = NULL, color_name = NULL, shape_name = NULL, dot_size = 1.5, alpha = 1, stroke = NULL, legend = TRUE, rotate_x = FALSE, rotate_y = FALSE, return_data = FALSE, show_variance = FALSE )
object |
a trained |
factors |
character or numeric specifying the factor(s) to plot, default is "all" |
covariates |
specifies sample covariate(s) to plot against: (1) a character giving the name of a column present in the sample covariates or sample metadata. (2) a character giving the name of a feature present in the training data. (3) a vector of the same length as the number of samples specifying continuous numeric values per sample. Default is the first sample covariates in covariates slot |
warped |
logical indicating whether to show the aligned covariate (default: TRUE), only relevant if warping has been used to align multiple sample groups |
show_missing |
(for 1-dim covariates) logical indicating whether to include samples for which |
scale |
logical indicating whether to scale factor values. |
color_by |
(for 1-dim covariates) specifies groups or values used to color the samples. This can be either: (1) a character giving the name of a feature present in the training data. (2) a character giving the same of a column present in the sample metadata. (3) a vector of the same length as the number of samples specifying discrete groups or continuous numeric values. |
shape_by |
(for 1-dim covariates) specifies groups or values used to shape the samples. This can be either: (1) a character giving the name of a feature present in the training data, (2) a character giving the same of a column present in the sample metadata. (3) a vector of the same length as the number of samples specifying discrete groups. |
color_name |
(for 1-dim covariates) name for color legend. |
shape_name |
(for 1-dim covariates) name for shape legend. |
dot_size |
(for 1-dim covariates) numeric indicating dot size. |
alpha |
(for 1-dim covariates) numeric indicating dot transparency. |
stroke |
(for 1-dim covariates) numeric indicating the stroke size |
legend |
(for 1-dim covariates) logical indicating whether to add legend. |
rotate_x |
(for spatial, 2-dim covariates) Rotate covariate on x-axis |
rotate_y |
(for spatial, 2-dim covariates) Rotate covariate on y-axis |
return_data |
logical indicating whether to return the data frame to plot instead of plotting |
show_variance |
(for 1-dim covariates) logical indicating whether to show the marginal variance of inferred factor values (only relevant for 1-dimensional covariates) |
To investigate the factors pattern along the covariates (such as time or a spatial coordinate) this function an be used to plot a scatterplot of the factor againt the values of each covariate
Returns a ggplot2
object
# Using an existing trained model file <- system.file("extdata", "MEFISTO_model.hdf5", package = "MOFA2") model <- load_model(file) plot_factors_vs_cov(model)