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Plot segmented regression

Source: R/plot_segments.R
plot_segments.Rd

Plot segmented regression results for specified features in each group, using the Trendy::plotFeature() function. The input is a list of SummarizedExperiment objects with no missing values and a list of Trendy analysis results for each group.

Usage

plot_segments(
  se_obj_imp_list,
  res_list,
  feature,
  group = NULL,
  nrow = NULL,
  ...
)

Arguments

se_obj_imp_list

A list of SummarizedExperiment objects with no missing values

res_list

A list of the Trendy analysis results, output of run_Trendy()

feature

A character vector of feature names to be plotted

group

A character vector of group names to be analysed. If NULL, all groups in the input list will be used (default is NULL)

nrow

Number of rows in the plot layout. If NULL and multiple features are provided, it will be set to half the number of features (rounded up) (default is NULL)

...

Additional arguments to be passed to the Trendy::plotFeature()

Value

Plots of the segmented regression fits for the specified features in each group.

Examples

data("example")
example_obj <- normalise_to_start(example_obj)
example_obj_list <- split_groups(example_obj)
example_obj_merged_list <- merge_replicates(example_obj_list)
example_obj_merged_list <-
    calc_feature_property(example_obj_merged_list, threshold = 0)
# no missing value in the example dataset, so imputation is not necessary
example_obj_merged_imp_list <- impute_groups(example_obj_merged_list)

# "untreated" group has only 3 time points, so Trendy analysis will not be
# performed for this group
# example_res_list <- run_Trendy(example_obj_merged_imp_list, maxK = 1,
#     minNumInSeg = 2, meanCut = 0)
data("example_res_list")

plot_segments(example_obj_merged_imp_list, example_res_list,
    feature = c("Mctp1"))
#> Plotting segmented regression for group: IFNbeta

#> Plotting segmented regression for group: IFNgamma

#> Plotting segmented regression for group: LPS

plot_breakpoints(example_res_list)
#> Warning: number of columns of result is not a multiple of vector length (arg 9)
#> Warning: number of columns of result is not a multiple of vector length (arg 3)
#> Warning: number of columns of result is not a multiple of vector length (arg 5)

trendy_summary <- summarise_Trendy(example_res_list)
#> Warning: number of columns of result is not a multiple of vector length (arg 9)
#> Warning: number of columns of result is not a multiple of vector length (arg 3)
#> Warning: number of columns of result is not a multiple of vector length (arg 5)
trendy_list <- extract_segment_trends(trendy_summary)