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Plot run discovery analysis

Source: R/plotting_functions.R
plot_run_discovery_analysis.Rd

plot_run_discovery_analysis() creates a visualization of the outcome of the discovery analysis. The visualization consists of four plots:

  • The upper left plot superimposes the discovery p-values (blue) on top of the negative control p-values (red) on an untransformed scale.

  • The upper right plot is the same as the upper left plot, but the scale is negative log-10 transformed. The discovery p-values ideally should trend above the diagonal line, indicating the presence of signal in the discovery set. The horizontal dashed line indicates the multiple testing threshold; discovery pairs whose p-value falls above this line are called as significant.

  • The bottom left panel is a volcano plot of the p-values and log fold changes of the discovery pairs. Each point corresponds to a pair; the estimated log-2 fold change of the pair is plotted on the horizontal axis, and the (negative log-10 transformed) p-value is plotted on the vertical axis. The horizontal dashed line again indicates the multiple testing threshold. Points above the dashed line (colored in purple) are called as discoveries, while points below (colored in blue) are called as insignificant.

  • The bottom right panel is a text box displaying the number of discovery pairs called as significant.

Usage

plot_run_discovery_analysis(
  sceptre_object,
  x_limits = c(-1.5, 1.5),
  point_size = 0.55,
  transparency = 0.8,
  return_indiv_plots = FALSE
)

Arguments

sceptre_object

a sceptre_object that has had run_discovery_analysis called on it

x_limits

(optional; default c(-1.5, 1.5)) a numeric vector of length 2 giving the lower and upper limits of the x-axis (corresponding to log-2 fold change) for the "Discovery volcano plot" panel

point_size

(optional; default 0.55) the size of the individual points in the plot

transparency

(optional; default 0.8) the transparency of the individual points in the plot

return_indiv_plots

(optional; default FALSE) if FALSE then a list of ggplot is returned; if TRUE then a single cowplot object is returned.

Value

a single cowplot object containing the combined panels (if return_indiv_plots is set to TRUE) or a list of the individual panels (if return_indiv_plots is set to FALSE)

Examples

data(highmoi_example_data)
data(grna_target_data_frame_highmoi)
# import data
sceptre_object <- import_data(
  response_matrix = highmoi_example_data$response_matrix,
  grna_matrix = highmoi_example_data$grna_matrix,
  grna_target_data_frame = grna_target_data_frame_highmoi,
  moi = "high",
  extra_covariates = highmoi_example_data$extra_covariates,
  response_names = highmoi_example_data$gene_names
)
positive_control_pairs <- construct_positive_control_pairs(sceptre_object)
discovery_pairs <- construct_cis_pairs(sceptre_object,
  positive_control_pairs = positive_control_pairs,
  distance_threshold = 5e6
)
sceptre_object |>
  set_analysis_parameters(
    side = "left",
    discovery_pairs = discovery_pairs,
    resampling_mechanism = "permutations",
  ) |>
  assign_grnas(method = "thresholding") |>
  run_qc() |>
  run_calibration_check() |>
  run_discovery_analysis() |>
  plot_run_discovery_analysis()
#> Note: If you are on a Mac laptop or desktop, consider setting `parallel = TRUE` to improve speed. Otherwise, keep `parallel = FALSE`.
#> Constructing negative control pairs.
#>  ✓
#> Generating permutation resamples.
#>  ✓
#> Analyzing pairs containing response ENSG00000253631 (1 of 98)
#> Analyzing pairs containing response ENSG00000100053 (5 of 98)
#> Analyzing pairs containing response ENSG00000100325 (10 of 98)
#> Analyzing pairs containing response ENSG00000253963 (15 of 98)
#> Analyzing pairs containing response ENSG00000100314 (20 of 98)
#> Analyzing pairs containing response ENSG00000177993 (25 of 98)
#> Analyzing pairs containing response ENSG00000099956 (30 of 98)
#> Analyzing pairs containing response ENSG00000253920 (35 of 98)
#> Analyzing pairs containing response ENSG00000203280 (40 of 98)
#> Analyzing pairs containing response ENSG00000187792 (45 of 98)
#> Analyzing pairs containing response ENSG00000211666 (50 of 98)
#> Analyzing pairs containing response ENSG00000236611 (55 of 98)
#> Analyzing pairs containing response ENSG00000253546 (60 of 98)
#> Analyzing pairs containing response ENSG00000099917 (65 of 98)
#> Analyzing pairs containing response ENSG00000253889 (70 of 98)
#> Analyzing pairs containing response ENSG00000099889 (75 of 98)
#> Analyzing pairs containing response ENSG00000241973 (80 of 98)
#> Analyzing pairs containing response ENSG00000225783 (85 of 98)
#> Analyzing pairs containing response ENSG00000279548 (90 of 98)
#> Analyzing pairs containing response ENSG00000100068 (95 of 98)
#> Note: If you are on a Mac laptop or desktop, consider setting `parallel = TRUE` to improve speed. Otherwise, keep `parallel = FALSE`.
#> Generating permutation resamples.
#>  ✓
#> Analyzing pairs containing response ENSG00000100218 (1 of 97)
#> Analyzing pairs containing response ENSG00000099958 (5 of 97)
#> Analyzing pairs containing response ENSG00000211638 (10 of 97)
#> Analyzing pairs containing response ENSG00000211685 (15 of 97)
#> Analyzing pairs containing response ENSG00000220891 (20 of 97)
#> Analyzing pairs containing response ENSG00000187905 (25 of 97)
#> Analyzing pairs containing response ENSG00000235954 (30 of 97)
#> Analyzing pairs containing response ENSG00000244486 (35 of 97)
#> Analyzing pairs containing response ENSG00000225783 (40 of 97)
#> Analyzing pairs containing response ENSG00000224277 (45 of 97)
#> Analyzing pairs containing response ENSG00000286326 (50 of 97)
#> Analyzing pairs containing response ENSG00000211672 (55 of 97)
#> Analyzing pairs containing response ENSG00000203280 (60 of 97)
#> Analyzing pairs containing response ENSG00000233521 (65 of 97)
#> Analyzing pairs containing response ENSG00000100319 (70 of 97)
#> Analyzing pairs containing response ENSG00000211674 (75 of 97)
#> Analyzing pairs containing response ENSG00000099917 (80 of 97)
#> Analyzing pairs containing response ENSG00000100053 (85 of 97)
#> Analyzing pairs containing response ENSG00000229770 (90 of 97)
#> Analyzing pairs containing response ENSG00000253920 (95 of 97)