Layer-level (group-level) boxplots

This function uses the output of sig_genes_extract_all() as well as the logcounts from the layer-level (group-level) data to visualize the expression of a given gene and display the modeling results for the given gene.

layer_boxplot(
  i = 1,
  sig_genes = sig_genes_extract(),
  short_title = TRUE,
  sce_layer = fetch_data(type = "sce_layer"),
  col_bkg_box = "grey80",
  col_bkg_point = "grey40",
  col_low_box = "violet",
  col_low_point = "darkviolet",
  col_high_box = "skyblue",
  col_high_point = "dodgerblue4",
  cex = 2,
  group_var = "layer_guess_reordered_short",
  assayname = "logcounts"
)

Arguments

i: A integer(1) indicating which row of sig_genes do you want to plot.
sig_genes: The output of sig_genes_extract_all().
short_title: A logical(1) indicating whether to print a short title or not.
sce_layer: Defaults to the output of fetch_data(type = 'sce_layer'). This is a SingleCellExperiment object with the spot-level Visium data compressed via pseudo-bulking to the layer-level (group-level) resolution. See fetch_data() for more details.
col_bkg_box: Box background color for layers not used when visualizing the pairwise model results.
col_bkg_point: Similar to col_bkg_box but for the points.
col_low_box: Box background color for layer(s) with the expected lower expression based on the actual test for row i of sig_genes.
col_low_point: Similar to col_low_box but for the points.
col_high_box: Similar to col_low_box but for the expected layer(s) with higher expression.
col_high_point: Similar to col_high_box but for the points.
cex: Controls the size of the text, points and axis legends.
group_var: A character(1) specifying a colData(sce_layer) column name to use for the x-axis.
assayname: A character(1) specifying the default assay to use from assays(sce_layer).

Value

This function creates a boxplot of the layer-level data (group-level) separated by layer and colored based on the model type from row i of sig_genes.

References

Adapted from https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/layer_specificity.R

Examples


## Obtain the necessary data
if (!exists("modeling_results")) {
    modeling_results <- fetch_data(type = "modeling_results")
}
#> 2024-12-16 21:51:52.075397 loading file /github/home/.cache/R/BiocFileCache/5db39a09009_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer")
#> 2024-12-16 21:51:53.325432 loading file /github/home/.cache/R/BiocFileCache/5db16a912b9_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1

## Top 2 genes from the enrichment model
sig_genes <- sig_genes_extract_all(
    n = 2,
    modeling_results = modeling_results,
    sce_layer = sce_layer
)

## Example default boxplot
set.seed(20200206)
layer_boxplot(sig_genes = sig_genes, sce_layer = sce_layer)


## Now show the long title version
set.seed(20200206)
layer_boxplot(
    sig_genes = sig_genes,
    short_title = FALSE,
    sce_layer = sce_layer
)


set.seed(20200206)
layer_boxplot(
    i = which(sig_genes$model_type == "anova")[1],
    sig_genes = sig_genes,
    sce_layer = sce_layer
)


set.seed(20200206)
layer_boxplot(
    i = which(sig_genes$model_type == "pairwise")[1],
    sig_genes = sig_genes,
    sce_layer = sce_layer
)


## Viridis colors displayed in the shiny app
library("viridisLite")
set.seed(20200206)
layer_boxplot(
    sig_genes = sig_genes,
    sce_layer = sce_layer,
    col_low_box = viridis(4)[2],
    col_low_point = viridis(4)[1],
    col_high_box = viridis(4)[3],
    col_high_point = viridis(4)[4]
)


## Paper colors displayed in the shiny app
set.seed(20200206)
layer_boxplot(
    sig_genes = sig_genes,
    sce_layer = sce_layer,
    col_low_box = "palegreen3",
    col_low_point = "springgreen2",
    col_high_box = "darkorange2",
    col_high_point = "orange1"
)


## Blue/red colors displayed in the shiny app
set.seed(20200206)
layer_boxplot(
    i = which(sig_genes$model_type == "pairwise")[1],
    sig_genes = sig_genes,
    sce_layer = sce_layer,
    col_bkg_box = "grey90",
    col_bkg_point = "grey60",
    col_low_box = "skyblue2",
    col_low_point = "royalblue3",
    col_high_box = "tomato2",
    col_high_point = "firebrick4",
    cex = 3
)

Arguments

Value

References

See also

Examples