Visualize GO enrichment test result in dot plot

Usage

plotGODot(
  result,
  group = NULL,
  query = c("Up", "Down"),
  pvalThresh = 0.05,
  n = 20,
  termIDMatch = "^GO",
  colorPalette = "E",
  colorDirection = 1,
  xlab = "-log10(P-value)",
  ylab = "Term name",
  ...
)

Arguments

result

Returned list object from runGOEnrich.

group

Character vector of group names, must be available in names(result). Default NULL make plots for all groups.

query

A single string selecting from which query to show the result. Choose from "Up" for results using up-regulated genes, "Down" for down-regulated genes. Default "Up".

pvalThresh

Numeric scalar, cutoff for p-value where smaller values are considered as significant. Default 0.05.

n

Number of top terms to be shown, ranked by p-value. Default 20.

termIDMatch

Regular expression pattern to match the term ID. Default "^GO" for only using GO terms from returned results.

colorPalette, colorDirection

Viridis palette options. Default "E" and 1.

xlab, ylab

Axis title for x and y axis. Default "-log10(P-value)" and "Term name", respectively.

...

Arguments passed on to .ggplotLigerTheme

legendColorTitle: Legend title text for color aesthetics, often used for categorical or continuous coloring of dots. Default NULL shows the original variable name.
legendSizeTitle: Legend title text for size aesthetics, often used for sizing dots by continuous variable. Default NULL shows the original variable name.
showLegend: Whether to show the legend. Default TRUE.
legendPosition: Text indicating where to place the legend. Choose from "top", "bottom", "left" or "right". Default "right".
baseSize: One-parameter control of all text sizes. Individual text element sizes can be controlled by other size arguments. "Title" sizes are 2 points larger than "text" sizes when being controlled by this.
titleSize,xTitleSize,yTitleSize,legendTitleSize: Size of main title, axis titles and legend title. Default NULL controls by baseSize + 2.
subtitleSize,xTextSize,yTextSize,legendTextSize: Size of subtitle text, axis texts and legend text. Default NULL controls by baseSize.
plotly: Whether to use plotly to enable web based interactive browsing for the plot. Requires installation of package "plotly". Default FALSE.

Value

A ggplot object if only one group or a list of ggplot objects.

Examples

# \donttest{
defaultCluster(pbmc) <- pbmcPlot$leiden_cluster
#> ℹ Storing given cluster labels to `cellMeta(x)` field: "defaultCluster".
# Test the DEG between "stim" and "ctrl", within each cluster
result <- runPairwiseDEG(
    pbmc,
    groupTest = "stim",
    groupCtrl = "ctrl",
    variable1 = "dataset",
    splitBy = "defaultCluster"
)
#> ℹ Running DEG within: "0"
#> ℹ Calling pairwise DESeq2 Wald test
#> ✔ Calling pairwise DESeq2 Wald test ... done
#> 
#> ℹ Running DEG within: "1"
#> ℹ Calling pairwise DESeq2 Wald test
#> -- note: fitType='parametric', but the dispersion trend was not well captured by the
#>    function: y = a/x + b, and a local regression fit was automatically substituted.
#>    specify fitType='local' or 'mean' to avoid this message next time.
#> ✔ Calling pairwise DESeq2 Wald test ... done
#> 
#> ℹ Running DEG within: "2"
#> ℹ Calling pairwise DESeq2 Wald test
#> ✔ Calling pairwise DESeq2 Wald test ... done
#> 
#> ℹ Running DEG within: "3"
#> ℹ Calling pairwise DESeq2 Wald test
#> ✔ Calling pairwise DESeq2 Wald test ... done
#> 
#> ℹ Running DEG within: "4"
#> ℹ Calling pairwise DESeq2 Wald test
#> ✔ Calling pairwise DESeq2 Wald test ... done
#> 
#> ℹ Running DEG within: "5"
#> ℹ Calling pairwise DESeq2 Wald test
#> ✔ Calling pairwise DESeq2 Wald test ... done
#> 
#> ℹ Running DEG within: "6"
#> ℹ Calling pairwise DESeq2 Wald test
#> ✔ Calling pairwise DESeq2 Wald test ... done
#> 
#> ℹ Running DEG within: "7"
#> ℹ Calling pairwise DESeq2 Wald test
#> ! Ignoring replicates (size in bracket) with too few cells: "others.ctrl.rep1 (2)"
#> ℹ Calling pairwise DESeq2 Wald test

#> ℹ Consider decrease minCellPerRep to exclude less replicates or/and lower nPsdRep to generate larger pseudo-replicates.
#> ℹ Calling pairwise DESeq2 Wald test

#> ✖ Error when computing on "7.stim": Too few replicates with more than 3 cells (`minCellPerRep`) for condition "others".
#> ℹ Calling pairwise DESeq2 Wald test

#> ! Empty result returned for this test.
#> ℹ Calling pairwise DESeq2 Wald test

#> ✖ Calling pairwise DESeq2 Wald test ... failed
#> 
# Setting `significant = FALSE` because it's hard for a gene list obtained
# from small test dataset to represent real-life biology.
if (requireNamespace("gprofiler2", quietly = TRUE)) {
    go <- runGOEnrich(result, group = "0.stim", splitReg = TRUE, significant = FALSE)
    # The toy example won't have significant result.
    plotGODot(go)
}
#> ! No enough matching terms (termIDMatch) nor significant terms (p-value <= 0.05) for group "0.stim".
#> list()
# }