chart.Correlation - Point shapes won't change with `pch`

[jay-sf]

Hi, we can't change the point shapes wit the pch.

Reproducible example:

library("PerformanceAnalytics")
chart.Correlation(iris[1:4], histogram=TRUE, pch = "+")

We can't see any + in the plot. Thanks for looking into this.

[Mako21]

See below for a version that supports pch and other plot options. I added ... to the two pairs calls.

chart.Correlation <- function (R, histogram = TRUE, method = c("pearson", "kendall", 
    "spearman"), ...) 
{
    x = checkData(R, method = "matrix")
    if (missing(method)) 
        method = method[1]
    panel.cor <- function(x, y, digits = 2, prefix = "", use = "pairwise.complete.obs", 
        method = "pearson", cex.cor, ...) {
        usr <- par("usr")
        on.exit(par(usr))
        par(usr = c(0, 1, 0, 1))
        r <- cor(x, y, use = use, method = method)
        txt <- format(c(r, 0.123456789), digits = digits)[1]
        txt <- paste(prefix, txt, sep = "")
        if (missing(cex.cor)) 
            cex <- 0.8/strwidth(txt)
        test <- cor.test(as.numeric(x), as.numeric(y), method = method)
        Signif <- symnum(test$p.value, corr = FALSE, na = FALSE, 
            cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1), symbols = c("***", 
                "**", "*", ".", " "))
        text(0.5, 0.5, txt, cex = cex * (abs(r) + 0.3)/1.3)
        text(0.8, 0.8, Signif, cex = cex, col = 2)
    }
    f <- function(t) {
        dnorm(t, mean = mean(x), sd = sd.xts(x))
    }
    dotargs <- list(...)
    dotargs$method <- NULL
    rm(method)
    hist.panel = function(x, ... = NULL) {
        par(new = TRUE)
        hist(x, col = "light gray", probability = TRUE, axes = FALSE, 
            main = "", breaks = "FD")
        lines(density(x, na.rm = TRUE), col = "red", lwd = 1)
        rug(x)
    }
    if (histogram) 
        pairs(x, gap = 0, lower.panel = panel.smooth, upper.panel = panel.cor, 
            diag.panel = hist.panel, ...)
    else pairs(x, gap = 0, lower.panel = panel.smooth, upper.panel = panel.cor, ...)
}

[braverock]

There is no sessionInfo here, but I'll assume from the context that this pertains to the latest PerformanceAnalytics that was just released to CRAN last week.

Those dots were removed specifically to deal with warnings generated by r-devel ahead of the CRAN release. So any change will need to not incur those warnings.

[DavorJ]

Any news on this one? If it can not be fixed, then at least remove the "..." argument from the documentation so people are not led astray.

[jay-sf]

Thanks @DavorJ for the reminder, apologies this escaped my attention in the hustle. + wont appear with PerformanceAnalytics 1.5.2. However @Mako21 's update on Mar 6, 2018 above is working fine for me. Below is a session info. Cheers!

R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] PerformanceAnalytics_1.5.2 xts_0.11-2                
[3] zoo_1.8-4                 

loaded via a namespace (and not attached):
[1] compiler_3.5.2  tools_3.5.2     yaml_2.2.0      grid_3.5.2     
[5] lattice_0.20-38 quadprog_1.5-5 

[braverock]

@peterccarl can you take a quick look at this and maybe apply?

[petitours]

Hi

I have the same problem reproducible example : chart.Correlation(iris[-5], bg=iris$Species, pch=21) pch remains = 1 regardless of the value used bg has no effect since pch must be between 21 and 25 col has no effect

Two year ago it worked very well Example I just found that works : https://www.r-bloggers.com/graphically-analyzing-variable-interactions-in-r/

This problem is blocking for me. It's terrible that something no longer works.

Thanks in advance

 R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C                   LC_TIME=French_France.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GGally_1.4.0               ggplot2_3.2.1              PerformanceAnalytics_1.5.3 xts_0.11-2                
[5] zoo_1.8-6                 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3         magrittr_1.5       hms_0.5.2          progress_1.2.2     munsell_0.5.0     
 [6] colorspace_1.4-1   lattice_0.20-38    R6_2.4.1           rlang_0.4.2        quadprog_1.5-8    
[11] stringr_1.4.0      plyr_1.8.5         tools_3.6.2        grid_3.6.2         gtable_0.3.0      
[16] withr_2.1.2        assertthat_0.2.1   lazyeval_0.2.2     tibble_2.1.3       lifecycle_0.1.0   
[21] crayon_1.3.4       farver_2.0.1       reshape2_1.4.3     RColorBrewer_1.1-2 vctrs_0.2.0       
[26] zeallot_0.1.0      labeling_0.3       stringi_1.4.3      compiler_3.6.2     pillar_1.4.2      
[31] prettyunits_1.0.2  scales_1.1.0       backports_1.1.5    reshape_0.8.8      pkgconfig_2.0.3

[chitrabaniya]

Hi is there any solutions to that same small font problem? I am having that same problem. Here is my sessioninfo:

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] PerformanceAnalytics_2.0.4 xts_0.12.1
[3] zoo_1.8-8 pvclust_2.2-0
[5] vegan_2.5-7 lattice_0.20-41
[7] permute_0.9-5

loaded via a namespace (and not attached): [1] knitr_1.31 cluster_2.1.0 splines_4.0.3 MASS_7.3-53
[5] rlang_0.4.10 quadprog_1.5-8 tcltk_4.0.3 tools_4.0.3
[9] parallel_4.0.3 grid_4.0.3 nlme_3.1-152 mgcv_1.8-33
[13] xfun_0.20 htmltools_0.5.1 yaml_2.2.1 digest_0.6.27
[17] bookdown_0.21 Matrix_1.2-18 evaluate_0.14 rmarkdown_2.6
[21] compiler_4.0.3