Plot the pairwise correlations between pairs of samples in a matrix. Histograms, correlation values, and smooth scatters with loess fits are visualized in each panel. Inspired by `methylKit::getCorrelation(..., plot=TRUE)` and examples in `pairs()`
Usage
plot_cor_pairs(
m,
hist_breaks = 30,
hist_col = "grey50",
cor_method = c("pearson", "kendall", "spearman"),
cor_use = "everything",
cor_digits = 2,
cor_cex = 2,
scatter_colramp = hcl.colors,
scatter_ab_col = "red2",
scatter_ab_lty = 2,
scatter_ab_lwd = 1,
scatter_crv_col = "red3",
scatter_crv_lwd = 2,
scatter_crv_lty = 1,
cex_labels = 2,
font_labels = 1
)Arguments
- m
Matrix with features in rows and Samples in columns
- hist_breaks
Number of breaks to use in histogram
- hist_col
Color of the histogram bars
- cor_method
Method to use for calculating correlations. One of "pearson" (default), "kendall", or "spearman": can be abbreviated
- cor_use
an optional character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs".
- cor_digits
Number of digits to report in correlations
- cor_cex
Character expansion size for correlation values
- scatter_colramp
function accepting an integer n as an argument and returning n colors used in the smoothScatter plots
- scatter_ab_col
Color of the abline of the smoothScatter plots
- scatter_ab_lty
Line type of the abline of the smoothScatter plots
- scatter_ab_lwd
Line weight of the abline of the smoothScatter plots
- scatter_crv_col
Color of the lowess lines of the smoothScatter plots
- scatter_crv_lwd
Line weight of the lowess lines of the smoothScatter plots
- scatter_crv_lty
Line type of the lowess lines of the smoothScatter plots
- cex_labels
Text panel graphics parameters passed to `pairs()`
- font_labels
Text panel graphics parameters passed to `pairs()`
