Violin plot with Bonferroni-adjusted Wilcoxon tests

library(canvasXpress)
y=read.table("https://www.canvasxpress.org/data/r/cX-statistics3-dat.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
x=read.table("https://www.canvasxpress.org/data/r/cX-statistics3-smp.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
canvasXpress(
data=y,
smpAnnot=x,
axisAlgorithm="rPretty",
axisTitleFontStyle="bold",
colorBy="Species",
colorScheme="Pastel",
graphOrientation="vertical",
graphType="Boxplot",
groupingFactors=list("Species"),
showBoxplotIfViolin=TRUE,
showLegend=FALSE,
showStatInference=TRUE,
showViolinBoxplot=TRUE,
smpTextRotate=0,
smpTitle="Species",
smpTitleFontStyle="bold",
statInference=list(annotate="padj", comparisons=list(list(groups=list("setosa", "versicolor"), p=8.34582714594074e-14), list(groups=list("versicolor", "virginica"), p=5.8690064106642e-07), list(groups=list("setosa", "virginica"), p=6.39669906939659e-17)), correction=list(method="bonferroni")),
title="Iris sepal length by species (Wilcoxon, Bonferroni-adjusted)",
xAxis=list("Sepal.Length"),
xAxisTitle="Sepal.Length"
)

from canvasxpress.canvas import CanvasXpress
from canvasxpress.plot import show_in_browser

if __name__ == "__main__":
  # Define the chart with its data and configuration
  chart: CanvasXpress = CanvasXpress(
    render_to = "statistics3",
    data = {
      "y": {
        "vars": ["Sepal.Length"],
        "smps": ["Obs1", "Obs2", "Obs3", "Obs4", "Obs5", "Obs6", "Obs7", "Obs8", "Obs9", "Obs10", "Obs11", "Obs12", "Obs13", "Obs14", "Obs15", "Obs16", "Obs17", "Obs18", "Obs19", "Obs20", "Obs21", "Obs22", "Obs23", "Obs24", "Obs25", "Obs26", "Obs27", "Obs28", "Obs29", "Obs30", "Obs31", "Obs32", "Obs33", "Obs34", "Obs35", "Obs36", "Obs37", "Obs38", "Obs39", "Obs40", "Obs41", "Obs42", "Obs43", "Obs44", "Obs45", "Obs46", "Obs47", "Obs48", "Obs49", "Obs50", "Obs51", "Obs52", "Obs53", "Obs54", "Obs55", "Obs56", "Obs57", "Obs58", "Obs59", "Obs60", "Obs61", "Obs62", "Obs63", "Obs64", "Obs65", "Obs66", "Obs67", "Obs68", "Obs69", "Obs70", "Obs71", "Obs72", "Obs73", "Obs74", "Obs75", "Obs76", "Obs77", "Obs78", "Obs79", "Obs80", "Obs81", "Obs82", "Obs83", "Obs84", "Obs85", "Obs86", "Obs87", "Obs88", "Obs89", "Obs90", "Obs91", "Obs92", "Obs93", "Obs94", "Obs95", "Obs96", "Obs97", "Obs98", "Obs99", "Obs100", "Obs101", "Obs102", "Obs103", "Obs104", "Obs105", "Obs106", "Obs107", "Obs108", "Obs109", "Obs110", "Obs111", "Obs112", "Obs113", "Obs114", "Obs115", "Obs116", "Obs117", "Obs118", "Obs119", "Obs120", "Obs121", "Obs122", "Obs123", "Obs124", "Obs125", "Obs126", "Obs127", "Obs128", "Obs129", "Obs130", "Obs131", "Obs132", "Obs133", "Obs134", "Obs135", "Obs136", "Obs137", "Obs138", "Obs139", "Obs140", "Obs141", "Obs142", "Obs143", "Obs144", "Obs145", "Obs146", "Obs147", "Obs148", "Obs149", "Obs150"],
        "data": [
          [5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6, 5, 4.4, 4.9, 5.4, 4.8, 4.8, 4.3, 5.8, 5.7, 5.4, 5.1, 5.7, 5.1, 5.4, 5.1, 4.6, 5.1, 4.8, 5, 5, 5.2, 5.2, 4.7, 4.8, 5.4, 5.2, 5.5, 4.9, 5, 5.5, 4.9, 4.4, 5.1, 5, 4.5, 4.4, 5, 5.1, 4.8, 5.1, 4.6, 5.3, 5, 7, 6.4, 6.9, 5.5, 6.5, 5.7, 6.3, 4.9, 6.6, 5.2, 5, 5.9, 6, 6.1, 5.6, 6.7, 5.6, 5.8, 6.2, 5.6, 5.9, 6.1, 6.3, 6.1, 6.4, 6.6, 6.8, 6.7, 6, 5.7, 5.5, 5.5, 5.8, 6, 5.4, 6, 6.7, 6.3, 5.6, 5.5, 5.5, 6.1, 5.8, 5, 5.6, 5.7, 5.7, 6.2, 5.1, 5.7, 6.3, 5.8, 7.1, 6.3, 6.5, 7.6, 4.9, 7.3, 6.7, 7.2, 6.5, 6.4, 6.8, 5.7, 5.8, 6.4, 6.5, 7.7, 7.7, 6, 6.9, 5.6, 7.7, 6.3, 6.7, 7.2, 6.2, 6.1, 6.4, 7.2, 7.4, 7.9, 6.4, 6.3, 6.1, 7.7, 6.3, 6.4, 6, 6.9, 6.7, 6.9, 5.8, 6.8, 6.7, 6.7, 6.3, 6.5, 6.2, 5.9]
        ]
      },
      "x": {
        "Species": ["setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica"]
      }
    },
    config = {
      "graphType": "Boxplot",
      "graphOrientation": "vertical",
      "groupingFactors": ["Species"],
      "xAxis": ["Sepal.Length"],
      "xAxisTitle": "Sepal.Length",
      "smpTitle": "Species",
      "smpTitleFontStyle": "bold",
      "axisTitleFontStyle": "bold",
      "axisAlgorithm": "rPretty",
      "smpTextRotate": 0,
      "showLegend": False,
      "colorBy": "Species",
      "title": "Iris sepal length by species (Wilcoxon, Bonferroni-adjusted)",
      "showStatInference": True,
      "statInference": {
        "correction": {
          "method": "bonferroni"
        },
        "annotate": "padj",
        "comparisons": [
          {
            "groups": ["setosa", "versicolor"],
            "p": 8.34582714594074e-14
          },
          {
            "groups": ["versicolor", "virginica"],
            "p": 5.8690064106642e-07
          },
          {
            "groups": ["setosa", "virginica"],
            "p": 6.39669906939659e-17
          }
        ]
      },
      "showViolinBoxplot": True,
      "showBoxplotIfViolin": True,
      "colorScheme": "Pastel"
    },
    width = 600,
    height = 600
  )

  # Display the chart in its own Web page
  show_in_browser(chart)

Run this notebook:

from canvasxpress.canvas import CanvasXpress
from canvasxpress.plot import graph

graph(
  CanvasXpress(
    render_to = "statistics3",
    data = {
      "y": {
        "vars": ["Sepal.Length"],
        "smps": ["Obs1", "Obs2", "Obs3", "Obs4", "Obs5", "Obs6", "Obs7", "Obs8", "Obs9", "Obs10", "Obs11", "Obs12", "Obs13", "Obs14", "Obs15", "Obs16", "Obs17", "Obs18", "Obs19", "Obs20", "Obs21", "Obs22", "Obs23", "Obs24", "Obs25", "Obs26", "Obs27", "Obs28", "Obs29", "Obs30", "Obs31", "Obs32", "Obs33", "Obs34", "Obs35", "Obs36", "Obs37", "Obs38", "Obs39", "Obs40", "Obs41", "Obs42", "Obs43", "Obs44", "Obs45", "Obs46", "Obs47", "Obs48", "Obs49", "Obs50", "Obs51", "Obs52", "Obs53", "Obs54", "Obs55", "Obs56", "Obs57", "Obs58", "Obs59", "Obs60", "Obs61", "Obs62", "Obs63", "Obs64", "Obs65", "Obs66", "Obs67", "Obs68", "Obs69", "Obs70", "Obs71", "Obs72", "Obs73", "Obs74", "Obs75", "Obs76", "Obs77", "Obs78", "Obs79", "Obs80", "Obs81", "Obs82", "Obs83", "Obs84", "Obs85", "Obs86", "Obs87", "Obs88", "Obs89", "Obs90", "Obs91", "Obs92", "Obs93", "Obs94", "Obs95", "Obs96", "Obs97", "Obs98", "Obs99", "Obs100", "Obs101", "Obs102", "Obs103", "Obs104", "Obs105", "Obs106", "Obs107", "Obs108", "Obs109", "Obs110", "Obs111", "Obs112", "Obs113", "Obs114", "Obs115", "Obs116", "Obs117", "Obs118", "Obs119", "Obs120", "Obs121", "Obs122", "Obs123", "Obs124", "Obs125", "Obs126", "Obs127", "Obs128", "Obs129", "Obs130", "Obs131", "Obs132", "Obs133", "Obs134", "Obs135", "Obs136", "Obs137", "Obs138", "Obs139", "Obs140", "Obs141", "Obs142", "Obs143", "Obs144", "Obs145", "Obs146", "Obs147", "Obs148", "Obs149", "Obs150"],
        "data": [
          [5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6, 5, 4.4, 4.9, 5.4, 4.8, 4.8, 4.3, 5.8, 5.7, 5.4, 5.1, 5.7, 5.1, 5.4, 5.1, 4.6, 5.1, 4.8, 5, 5, 5.2, 5.2, 4.7, 4.8, 5.4, 5.2, 5.5, 4.9, 5, 5.5, 4.9, 4.4, 5.1, 5, 4.5, 4.4, 5, 5.1, 4.8, 5.1, 4.6, 5.3, 5, 7, 6.4, 6.9, 5.5, 6.5, 5.7, 6.3, 4.9, 6.6, 5.2, 5, 5.9, 6, 6.1, 5.6, 6.7, 5.6, 5.8, 6.2, 5.6, 5.9, 6.1, 6.3, 6.1, 6.4, 6.6, 6.8, 6.7, 6, 5.7, 5.5, 5.5, 5.8, 6, 5.4, 6, 6.7, 6.3, 5.6, 5.5, 5.5, 6.1, 5.8, 5, 5.6, 5.7, 5.7, 6.2, 5.1, 5.7, 6.3, 5.8, 7.1, 6.3, 6.5, 7.6, 4.9, 7.3, 6.7, 7.2, 6.5, 6.4, 6.8, 5.7, 5.8, 6.4, 6.5, 7.7, 7.7, 6, 6.9, 5.6, 7.7, 6.3, 6.7, 7.2, 6.2, 6.1, 6.4, 7.2, 7.4, 7.9, 6.4, 6.3, 6.1, 7.7, 6.3, 6.4, 6, 6.9, 6.7, 6.9, 5.8, 6.8, 6.7, 6.7, 6.3, 6.5, 6.2, 5.9]
        ]
      },
      "x": {
        "Species": ["setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica"]
      }
    },
    config = {
      "graphType": "Boxplot",
      "graphOrientation": "vertical",
      "groupingFactors": ["Species"],
      "xAxis": ["Sepal.Length"],
      "xAxisTitle": "Sepal.Length",
      "smpTitle": "Species",
      "smpTitleFontStyle": "bold",
      "axisTitleFontStyle": "bold",
      "axisAlgorithm": "rPretty",
      "smpTextRotate": 0,
      "showLegend": False,
      "colorBy": "Species",
      "title": "Iris sepal length by species (Wilcoxon, Bonferroni-adjusted)",
      "showStatInference": True,
      "statInference": {
        "correction": {
          "method": "bonferroni"
        },
        "annotate": "padj",
        "comparisons": [
          {
            "groups": ["setosa", "versicolor"],
            "p": 8.34582714594074e-14
          },
          {
            "groups": ["versicolor", "virginica"],
            "p": 5.8690064106642e-07
          },
          {
            "groups": ["setosa", "virginica"],
            "p": 6.39669906939659e-17
          }
        ]
      },
      "showViolinBoxplot": True,
      "showBoxplotIfViolin": True,
      "colorScheme": "Pastel"
    },
    width = 600,
    height = 600
  )
)

using CanvasXpress

canvasxpress(Dict(
  "y" => Dict(
    "vars" => ["Sepal.Length"],
    "smps" => ["Obs1", "Obs2", "Obs3", "Obs4", "Obs5", "Obs6", "Obs7", "Obs8", "Obs9", "Obs10", "Obs11", "Obs12", "Obs13", "Obs14", "Obs15", "Obs16", "Obs17", "Obs18", "Obs19", "Obs20", "Obs21", "Obs22", "Obs23", "Obs24", "Obs25", "Obs26", "Obs27", "Obs28", "Obs29", "Obs30", "Obs31", "Obs32", "Obs33", "Obs34", "Obs35", "Obs36", "Obs37", "Obs38", "Obs39", "Obs40", "Obs41", "Obs42", "Obs43", "Obs44", "Obs45", "Obs46", "Obs47", "Obs48", "Obs49", "Obs50", "Obs51", "Obs52", "Obs53", "Obs54", "Obs55", "Obs56", "Obs57", "Obs58", "Obs59", "Obs60", "Obs61", "Obs62", "Obs63", "Obs64", "Obs65", "Obs66", "Obs67", "Obs68", "Obs69", "Obs70", "Obs71", "Obs72", "Obs73", "Obs74", "Obs75", "Obs76", "Obs77", "Obs78", "Obs79", "Obs80", "Obs81", "Obs82", "Obs83", "Obs84", "Obs85", "Obs86", "Obs87", "Obs88", "Obs89", "Obs90", "Obs91", "Obs92", "Obs93", "Obs94", "Obs95", "Obs96", "Obs97", "Obs98", "Obs99", "Obs100", "Obs101", "Obs102", "Obs103", "Obs104", "Obs105", "Obs106", "Obs107", "Obs108", "Obs109", "Obs110", "Obs111", "Obs112", "Obs113", "Obs114", "Obs115", "Obs116", "Obs117", "Obs118", "Obs119", "Obs120", "Obs121", "Obs122", "Obs123", "Obs124", "Obs125", "Obs126", "Obs127", "Obs128", "Obs129", "Obs130", "Obs131", "Obs132", "Obs133", "Obs134", "Obs135", "Obs136", "Obs137", "Obs138", "Obs139", "Obs140", "Obs141", "Obs142", "Obs143", "Obs144", "Obs145", "Obs146", "Obs147", "Obs148", "Obs149", "Obs150"],
    "data" => [
      [5.1, 4.9, 4.7, 4.6, 5, 5.4, 4.6, 5, 4.4, 4.9, 5.4, 4.8, 4.8, 4.3, 5.8, 5.7, 5.4, 5.1, 5.7, 5.1, 5.4, 5.1, 4.6, 5.1, 4.8, 5, 5, 5.2, 5.2, 4.7, 4.8, 5.4, 5.2, 5.5, 4.9, 5, 5.5, 4.9, 4.4, 5.1, 5, 4.5, 4.4, 5, 5.1, 4.8, 5.1, 4.6, 5.3, 5, 7, 6.4, 6.9, 5.5, 6.5, 5.7, 6.3, 4.9, 6.6, 5.2, 5, 5.9, 6, 6.1, 5.6, 6.7, 5.6, 5.8, 6.2, 5.6, 5.9, 6.1, 6.3, 6.1, 6.4, 6.6, 6.8, 6.7, 6, 5.7, 5.5, 5.5, 5.8, 6, 5.4, 6, 6.7, 6.3, 5.6, 5.5, 5.5, 6.1, 5.8, 5, 5.6, 5.7, 5.7, 6.2, 5.1, 5.7, 6.3, 5.8, 7.1, 6.3, 6.5, 7.6, 4.9, 7.3, 6.7, 7.2, 6.5, 6.4, 6.8, 5.7, 5.8, 6.4, 6.5, 7.7, 7.7, 6, 6.9, 5.6, 7.7, 6.3, 6.7, 7.2, 6.2, 6.1, 6.4, 7.2, 7.4, 7.9, 6.4, 6.3, 6.1, 7.7, 6.3, 6.4, 6, 6.9, 6.7, 6.9, 5.8, 6.8, 6.7, 6.7, 6.3, 6.5, 6.2, 5.9]
    ]
  ),
  "x" => Dict(
    "Species" => ["setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "setosa", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "versicolor", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica", "virginica"]
  )
);
  graphType = "Boxplot",
  graphOrientation = "vertical",
  groupingFactors = ["Species"],
  xAxis = ["Sepal.Length"],
  xAxisTitle = "Sepal.Length",
  smpTitle = "Species",
  smpTitleFontStyle = "bold",
  axisTitleFontStyle = "bold",
  axisAlgorithm = "rPretty",
  smpTextRotate = 0,
  showLegend = false,
  colorBy = "Species",
  title = "Iris sepal length by species (Wilcoxon, Bonferroni-adjusted)",
  showStatInference = true,
  statInference = Dict(
    "correction" => Dict(
      "method" => "bonferroni"
    ),
    "annotate" => "padj",
    "comparisons" => [
      Dict(
        "groups" => ["setosa", "versicolor"],
        "p" => 8.34582714594074e-14
      ),
      Dict(
        "groups" => ["versicolor", "virginica"],
        "p" => 5.8690064106642e-07
      ),
      Dict(
        "groups" => ["setosa", "virginica"],
        "p" => 6.39669906939659e-17
      )
    ]
  ),
  showViolinBoxplot = true,
  showBoxplotIfViolin = true,
  colorScheme = "Pastel"
)