Examples
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-Data Preparation
-Examples here use data manipulated with the tidyverse related packages (dplyr, tibble, etc). This is just one way to manipulate data into the correct format to plot in CanvasXpress.
-A variety of commonly-used canvasXpress options are used below to provide examples of how to position, resize and configure various aspects of the charts from the call to the CanvasXpress function in R. This includes items such as the Axis Titles, Legends, Colors, etc. All of these optional parameters are documented on the main CanvasXpress site at http://canvasXpress.org.
-library(canvasXpress)
-library(dplyr)
-library(tibble)
-library(tidyr)
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-data <- USArrests %>%
- rownames_to_column(var = "State") %>%
- mutate(Total = (Assault + Rape + Murder),
- Category = cut(Total, 3,
- labels = c("low", "med", "high"),
- ordered_result = T))
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-Scatter 2D Chart
-cxdata <- data %>% select(Murder, Assault)
-cxdata.varAnnot <- data %>% select(UrbanPop, Category)
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-rownames(cxdata) <- data[, "State"]
-rownames(cxdata.varAnnot) <- data[, "State"]
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-canvasXpress(data = cxdata,
- varAnnot = cxdata.varAnnot,
- graphType = "Scatter2D",
- colorBy = "UrbanPop",
- shapeBy = "Category",
- legendPosition = "right",
- legendOrder = list("Category" = list("low", "med", "high")),
- title = "Murder vs Assault Rates",
- titleScaleFontFactor = 0.5)
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-Scatter2D
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-Stacked Bar Chart
-cxdata <- t(data %>% select(Assault, Rape, Murder))
-colnames(cxdata) <- data$State
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-canvasXpress(data = cxdata,
- graphType = "Stacked",
- colorScheme = "Blues",
- graphOrientation = "vertical",
- legendInside = TRUE,
- legendPosition = "topRight",
- smpLabelRotate = 20,
- title = "US Arrests by State and Type",
- titleScaleFontFactor = 0.5,
- xAxisTitle = "Total Arrests",
- xAxis2Title = "Total Arrests")
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-StackedBar
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-Clustered Bar Chart
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-CanvasXpress clustering
-cxdata <- t(data %>% select(Assault, Rape, Murder))
-colnames(cxdata) <- data$State
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-canvasXpress(data = cxdata,
- graphType = "Stacked",
- graphOrientation = "horizontal",
- colorScheme = "Reds",
- showSampleNames = FALSE,
- title = "Clustered Arrests",
- subtitle = "(by State and Type)",
- titleScaleFontFactor = 0.5,
- subtitleScaleFontFactor = 0.25,
- xAxisShow = FALSE,
- xAxis2Title = "Total Arrests",
- legendPosition = "bottom",
- legendColumns = 3,
-#canvasXpress clustering options
- samplesClustered = TRUE,
- linkage = "single",
- distance = "manhattan",
- smpDendrogramPosition = "left")
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-ClusteredBar1
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-Preclustered data in Newick format
-cxdata <- t(data %>% select(Assault, Rape, Murder))
-colnames(cxdata) <- data$State
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-cxdata.tree <- list("smps" = "((8,32):20.2,(((4,((0,7):14.7,(23,(1,(27,(21,(31,(12,17):6.8):7.8):11.0):14.0):14.7):15.8):16.2):17.9,(39,(30,(2,19):12.4):13.4):18.6):19.9,(((11,(6,(((34,43):5.6,(13,15):6.2):7.5,(26,(37,(16,25):3.8):4.8):7.6):7.6):9.0):9.3,((10,(33,(44,(48,(14,28):2.9):3.9):5.8):8.3):14.1,(22,(40,(18,47):7.1):9.7):17.2):20.1):20.2,((5,(24,(9,(42,(3,41):13.8):14.9):15.0):15.5):21.0,(38,(46,(36,(20,(35,(45,(29,49):5.8):6.0):7.6):7.9):13.0):14.3):23.7):24.2):29.1):33.8):43.2"
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-canvasXpress(data = cxdata,
- graphType = "Stacked",
- graphOrientation = "horizontal",
- colorScheme = "Reds",
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- showSampleNames = FALSE,
- title = "Clustered Arrests",
- subtitle = "(by State and Type)",
- titleScaleFontFactor = 0.5,
- subtitleScaleFontFactor = 0.25,
- xAxisShow = FALSE,
- xAxis2Title = "Total Arrests",
- legendPosition = "bottomRight",
- legendInside = TRUE,
-#user-provided clustering options
- newickData = cxdata.tree,
- smpDendrogramPosition = "left",
- showSmpDendrogram = TRUE)
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-ClusteredBar2
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-BoxPlot
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-CanvasXpress statistics
-reshape <- data %>% gather(key = "Type", value = "Rate",
- Assault, Rape, Murder)
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-cxdata <- t(reshape %>% select(Rate))
-cxdata.smpAnnot <- t(reshape %>% select(Type))
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-colnames(cxdata.smpAnnot) <- colnames(cxdata)
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-canvasXpress(data = cxdata,
- smpAnnot = cxdata.smpAnnot,
- graphType = "Boxplot",
- colorScheme = "Pastel",
- graphOrientation = "vertical",
- groupingFactors = list("Type"),
- smpLabelFontStyle = "italic",
- smpLabelRotate = 90,
- showLegend = FALSE,
- title = "US Arrests by Type",
- titleScaleFontFactor = 0.5,)
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-BoxPlot1
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-Precalculated statistics
-precalc.stats <- apply(data %>% select(Assault, Rape, Murder), 2, boxplot.stats)
-precalc.data <- as.data.frame(lapply(precalc.stats, function(x) { x$stats }))
-precalc.out <- data.frame(lapply(precalc.stats, function(x) { paste(x$out, collapse=',') }), stringsAsFactors = F)
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-cxdata <- precalc.data %>% mutate_all(as.character)
-cxdata <- bind_rows(cxdata, precalc.out)
-rownames(cxdata) <- c("iqr1", "qtl1", "median", "qtl3", "iqr3", "outliers")
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-canvasXpress(data = cxdata,
- graphType = "Boxplot",
- boxplotGroupData = "Type",
- colorScheme = "Pastel",
- graphOrientation = "vertical",
- groupingFactors = list("Type"),
- smpLabelFontStyle = "italic",
- smpLabelRotate = 90,
- showLegend = FALSE,
- title = "US Arrests by Type",
- titleScaleFontFactor = 0.5,)
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-BoxPlot2
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