GitHub - kevinblighe/CorLevelPlot: Visualise correlation results and test significancies of these (original) (raw)
Visualise correlation results and test significancies of these
Kevin Blighe 2019-01-29
- Example CorLevelPlot plots
- Example 1: WGCNA (weighted gene co-expression network analysis) simulated data:
- Example 2: Iris dataset principal components analysis:
- Example 3: World Health Organization (WHO) MONICA data:
- Acknowledgments
- Session info
- References
CorLevelPlot provides a quick and colourful way to visualise statistically significant correlations between any combination of categorical and continuous variables. Moreover, the statistical significancies of these correlations are also provided.
Example CorLevelPlot plots
Install and load CorLevelPlot:
devtools::install_github("kevinblighe/CorLevelPlot")Example 1: WGCNA (weighted gene co-expression network analysis) simulated data:
The following code taken from Tutorial for the WGCNA package for R - 1. Simulation of expression and trait data
# simulate trait-to-eigengene data
no.obs <- 50
ESturquoise <- 0; ESbrown <- -0.6; ESgreen <- 0.6; ESyellow <- 0
ESvector <- c(ESturquoise, ESbrown, ESgreen, ESyellow)
nGenes1 <- 3000
simulateProportions1 <- c(0.2, 0.15, 0.08, 0.06, 0.04)
set.seed(1)
MEgreen <- rnorm(no.obs)
scaledy <- MEgreen * ESgreen + sqrt(1 - ESgreen ^ 2) * rnorm(no.obs)
y <- ifelse( scaledy > median(scaledy), 2, 1)
MEturquoise <- ESturquoise * scaledy + sqrt(1 - ESturquoise ^ 2) * rnorm(no.obs)
MEblue <- 0.6 * MEturquoise + sqrt(1 - 0.6 ^ 2) * rnorm(no.obs)
MEbrown <- ESbrown * scaledy + sqrt(1 - ESbrown ^ 2) * rnorm(no.obs)
MEyellow <- ESyellow * scaledy + sqrt(1 - ESyellow ^ 2) * rnorm(no.obs)
ModuleEigengeneNetwork1 <- data.frame(y, MEturquoise, MEblue, MEbrown, MEgreen, MEyellow)
CorLevelPlot(data = ModuleEigengeneNetwork1,
x = c("y", "MEturquoise", "MEblue", "MEbrown", "MEgreen", "MEyellow"),
y = c("y", "MEturquoise", "MEblue", "MEbrown", "MEgreen", "MEyellow"),
titleX = "X correlates",
cexTitleX = 3.0,
rotTitleX = 0,
colTitleX = "forestgreen",
fontTitleX = 2,
titleY = "Y\ncorrelates",
cexTitleY = 4.0,
rotTitleY = 100,
colTitleY = "gold",
fontTitleY = 4,
cexLabX = 1.0,
rotLabX = 45,
colLabX = "grey20",
fontLabX = 1,
cexLabY = 1.0,
rotLabY = 30,
colLabY = "royalblue",
fontLabY = 1,
posLab = "bottomleft",
col = c("blue4", "blue3", "blue2", "blue1", "white", "red1", "red2", "red3", "red4"),
posColKey = "right",
cexLabColKey = 1.2,
cexCorval = 1.0,
fontCorval = 4,
main = "WGCNA example",
scale = FALSE,
cexMain = 2,
rotMain = 360,
colMain = "red4",
fontMain = 4,
corFUN = "pearson",
corUSE = "pairwise.complete.obs",
signifSymbols = c("***", "**", "*", ""),
signifCutpoints = c(0, 0.001, 0.01, 0.05, 1),
colFrame = "white",
plotRsquared = FALSE)
Example 2: Iris dataset principal components analysis:
library(datasets)
data(iris)
# order the categories in the 'Species' column
# CorLevelPlot will conver these to 1, 2, 3, ...
iris$Species <- as.numeric(factor(iris$Species, levels=c("setosa", "versicolor", "virginica")))
i <- CorLevelPlot(data = iris,
x = c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width", "Species"),
y = c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width", "Species"),
col = c("white", "cornsilk1", "yellow", "gold", "forestgreen", "darkgreen"),
cexCorval = 1.2,
fontCorval = 2,
posLab = "all",
rotLabX = 45,
scale = TRUE,
main = bquote(Iris~r^2~correlates),
plotRsquared = TRUE)
pca <- stats::prcomp(iris[,c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")])
df <- data.frame(pca$x, iris)
ii <- CorLevelPlot(data = df,
x = c("PC1", "PC2", "PC3", "PC4"),
y = c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width", "Species"),
cexTitleX = 2.0,
rotTitleX = 0,
fontTitleX = 2,
titleY = "Iris components",
cexTitleY = 2.0,
rotTitleY = 90,
fontTitleY = 2,
posLab = "topright",
col = c("blue1", "skyblue", "white", "pink", "red1"),
posColKey = "bottom",
cexLabColKey = 1.5,
cexCorval = 1.5,
fontCorval = 2,
rotLabX = 45,
scale = TRUE,
main = "Iris PC correlates",
colFrame = "white",
plotRsquared = FALSE)
require(rasterVis)
require(gridExtra)
require(grid)
grid.arrange(
arrangeGrob(i,
top = textGrob("A",
x = unit(0.05,"npc"),
y = unit(0.9,"npc"),
just = c("left","top"),
gp = gpar(fontsize=32))),
arrangeGrob(ii,
top = textGrob("B",
x = unit(0.05,"npc"),
y = unit(0.9,"npc"),
just = c("left","top"),
gp = gpar(fontsize=32))),
ncol = 2)
Example 3: World Health Organization (WHO) MONICA data:
library(DAAG)
data(monica)
# order the categorical variables
monica$outcome <- as.numeric(factor(monica$outcome, levels=c("dead", "live")))
monica$diabetes[monica$diabetes=="nk"] <- NA
monica$diabetes <- as.numeric(factor(monica$diabetes, levels=c("n", "y")))
monica$hichol[monica$hichol=="nk"] <- NA
monica$hichol <- as.numeric(factor(monica$hichol, levels=c("n", "y")))
monica$stroke[monica$stroke=="nk"] <- NA
monica$stroke <- as.numeric(factor(monica$stroke, levels=c("n", "y")))
monica$sex <- as.numeric(factor(monica$sex, levels=c("m", "f")))
monica$yronset <- as.numeric(factor(monica$yronset, levels=c("85","86","87","88","89","90","91","92","93")))
monica$highbp[monica$highbp=="nk"] <- NA
monica$highbp <- as.numeric(factor(monica$highbp, levels=c("n", "y")))
monica$angina[monica$angina=="nk"] <- NA
monica$angina <- as.numeric(factor(monica$angina, levels=c("n", "y")))
monica$hosp <- as.numeric(factor(monica$hosp, levels=c("n", "y")))
CorLevelPlot(data = monica,
x = c("outcome", "diabetes", "highbp", "hichol", "angina", "hosp"),
y = c("sex", "age", "yronset"),
col = c("darkblue", "blue2", "black", "red2", "darkred"),
cexCorval = 1.5,
colCorval = "white",
fontCorval = 2,
posLab = "bottomleft",
rotLabX = 45,
posColKey = "top",
cexLabColKey = 1.2,
scale = TRUE,
main = "World Health Organization",
colFrame = "white",
plotRsquared = FALSE)
Session info
## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
## LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
##
## locale:
## [1] LC_CTYPE=pt_BR.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=pt_BR.UTF-8
## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=pt_BR.UTF-8
## [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] DAAG_1.22 gridExtra_2.3 rasterVis_0.45
## [4] latticeExtra_0.6-28 RColorBrewer_1.1-2 lattice_0.20-38
## [7] raster_2.8-4 sp_1.3-1 BiocInstaller_1.32.1
## [10] CorLevelPlot_0.99.0 knitr_1.21
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.0 compiler_3.5.2 highr_0.7
## [4] prettyunits_1.0.2 remotes_2.0.2 tools_3.5.2
## [7] digest_0.6.18 pkgbuild_1.0.2 pkgload_1.0.2
## [10] gtable_0.2.0 viridisLite_0.3.0 evaluate_0.12
## [13] memoise_1.1.0 rlang_0.3.1 cli_1.0.1
## [16] parallel_3.5.2 curl_3.3 yaml_2.2.0
## [19] hexbin_1.27.2 xfun_0.4 withr_2.1.2
## [22] stringr_1.3.1 desc_1.2.0 fs_1.2.6
## [25] devtools_2.0.1 rprojroot_1.3-2 glue_1.3.0
## [28] R6_2.3.0 processx_3.2.1 rmarkdown_1.11
## [31] sessioninfo_1.1.1 callr_3.1.1 magrittr_1.5
## [34] codetools_0.2-16 backports_1.1.3 ps_1.3.0
## [37] htmltools_0.3.6 usethis_1.4.0 assertthat_0.2.0
## [40] stringi_1.2.4 crayon_1.3.4 zoo_1.8-4
References
(Blighe 2018)
Blighe, Kevin. 2018. “CorLevelPlot: Visualise correlation results and test significancies of these.” https://github.com/kevinblighe.