How to change the scatter plot as I required?

[Muhid]

Hi everyone,
I prepared the following scatter plot using the codes below-

df <- Box[1:254, 2:13]
panel.cor <- function(x, y, digits=2, prefix="", cex.cor, ...)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(0, 1, 0, 1))
r <- abs(cor(x, y, use="complete.obs"))
txt <- format(c(r, 0.123456789), digits=digits)[1]
test <- cor.test(x,y)
Signif <- ifelse(round(test$p.value,3)<0.001,"p<0.001",paste("p=",round(test$p.value,3)))
text(0.5, 0.25, paste("r=",txt))
text(.5, .75, Signif)
}

panel.hist <- function(x, ...)
{
usr <- par("usr"); on.exit(par(usr))
par(usr = c(usr[1:2], 0, 1.5) )
h <- hist(x, plot = FALSE)
breaks <- h$breaks; nB <- length(breaks)
y <- h$counts; y <- y/max(y)
rect(breaks[-nB], 0, breaks[-1], y, col="cyan", ...)
}

panel<-function(x,y, col=c("#00BFFF", "#FF9933"), cex = 0.8, pch = par("pch"), span = 2/3, iter = 3, ...)
{
points(x,y, col=col, cex=cex, pch=pch)
abline(lm(y~x), col='red')
}

pairs(df,
lower.panel=panel, upper.panel=panel.cor,diag.panel=panel.hist)

And this is my sample data-

Treatment	SL	RL	SFW	RFW	SDW	RDW	STWC	RTWC	RSR	SVI	LRWC	CMS
Control	14.43	14.01	69.57	36.84	11.58	8.59	83.36	76.68	0.74	9.39	62.8	55.6
PEG (25%)	6.97	7.34	31.86	26.44	8.08	6.99	74.64	73.56	0.87	4.82	50.3	39.3
Control	12.92	8.96	65.33	65.59	7.77	6.12	88.10	90.67	0.79	8.09	71.7	57.8
PEG (25%)	8.11	5.86	21.90	48.34	4.81	5.24	78.05	89.16	1.09	5.09	58.4	43.6
Control	17.85	8.88	98.37	65.39	9.44	6.82	90.40	89.56	0.72	11.13	74.1	62.1
PEG (25%)	9.26	5.38	41.11	46.39	5.81	5.84	85.87	87.42	1.00	6.09	54.2	44.8
Control	11.94	9.91	68.06	37.37	7.88	7.04	88.43	81.17	0.89	7.20	68.4	60.0
PEG (25%)	7.71	5.80	35.56	22.59	5.52	5.84	84.47	74.14	1.06	4.54	54.2	41.9
Control	13.12	9.89	93.54	49.99	9.73	7.60	89.60	84.79	0.78	14.79	75.4	65.7
PEG (25%)	12.39	6.95	64.27	39.55	8.34	6.83	87.02	82.73	0.82	12.43	67.4	51.5
Control	13.79	8.80	75.82	46.65	8.34	7.49	89.01	83.95	0.90	15.72	63.8	57.3
PEG (25%)	7.89	5.56	39.51	36.36	5.27	6.79	86.65	81.33	1.29	9.33	51.6	39.8
Control	11.53	10.46	74.57	46.91	9.30	6.87	87.53	85.35	0.74	7.40	71.6	60.0
PEG (25%)	7.65	6.81	37.25	28.88	6.43	5.86	82.74	79.71	0.91	4.78	59.3	40.5
Control	16.26	15.57	83.83	57.73	8.11	6.89	90.32	88.07	0.85	12.53	67.3	62.1
PEG (25%)	7.01	7.53	40.61	44.63	5.10	5.77	87.44	87.07	1.13	5.74	54.9	45.0
Control	13.63	8.51	93.31	33.72	9.16	7.28	90.18	78.42	0.79	10.18	73.2	52.8
PEG (25%)	6.61	4.96	43.24	18.41	6.38	5.65	85.25	69.33	0.89	5.27	56.8	38.9
Control	15.81	11.54	88.62	49.47	9.81	6.42	88.93	87.02	0.65	21.07	77.8	72.4

I need some changes in the plot-

1. Want to add two smooth lines for two treatments/levels in each box of the lower panel,
2. In the upper panel, I want add two r values for two treatment/levels in each box,
3. Want to add significance level by asterisk mark with r values instead of text.
4. Text size sufficiently bigger so that it can be easily understood.
5. If possible, a curve to add with the histogram in the diagonal panel.

If someone here rewrite/amend the provided code using my sample data, I will be grateful.
Thanks everyone

[williaml]

@Muhid

df <- Box[1:254, 2:13]

We don't have access to Box. Can you make it reproducible?

FAQ: What's a reproducible example (`reprex`) and how do I create one?

Why reprex? Getting unstuck is hard. Your first step here is usually to create a reprex, or reproducible example. The goal of a reprex is to package your code, and information about your problem so that others can run it and feel your pain. Then, hopefully, folks can more easily provide a solution. What's in a Reproducible Example? Parts of a reproducible example: background information - Describe what you are trying to do. What have you already done? complete set up - include any library() calls and data to reproduce your issue. data for a reprex: Here's a discussion on setting up data for a reprex make it run - include the minimal code required to reproduce your error on the data…

You could also just use something like ggpairs.

ggplot2 generalized pairs plot — ggpairs

[Muhid]

Thanks @williaml
Here is the reproducible data that I used-
structure(list(Treatment = c("Control", "PEG (25%)", "Control",
"PEG (25%)", "Control", "PEG (25%)", "Control", "PEG (25%)",
"Control", "PEG (25%)"), SL = c(14.43, 6.97, 12.92, 8.11, 17.85,
9.26, 11.94, 7.71, 13.12, 12.39), RL = c(14.01, 7.34, 8.96, 5.86,
8.88, 5.38, 9.91, 5.8, 9.89, 6.95), SFW = c(69.57, 31.86, 65.33,
21.9, 98.37, 41.11, 68.06, 35.56, 93.54, 64.27), RFW = c(36.84,
26.44, 65.59, 48.34, 65.39, 46.39, 37.37, 22.59, 49.99, 39.55
), SDW = c(11.58, 8.08, 7.77, 4.81, 9.44, 5.81, 7.88, 5.52, 9.73,
8.34), RDW = c(8.59, 6.99, 6.12, 5.24, 6.82, 5.84, 7.04, 5.84,
7.6, 6.83), STWC = c(83.36, 74.64, 88.1, 78.05, 90.4, 85.87,
88.43, 84.47, 89.6, 87.02), RTWC = c(76.68, 73.56, 90.67, 89.16,
89.56, 87.42, 81.17, 74.14, 84.79, 82.73), RSR = c(0.74, 0.87,
0.79, 1.09, 0.72, 1, 0.89, 1.06, 0.78, 0.82), SVI = c(9.39, 4.82,
8.09, 5.09, 11.13, 6.09, 7.2, 4.54, 14.79, 12.43), LRWC = c(62.8,
50.3, 71.7, 58.4, 74.1, 54.2, 68.4, 54.2, 75.4, 67.4), CMS = c(55.6,
39.3, 57.8, 43.6, 62.1, 44.8, 60, 41.9, 65.7, 51.5)), row.names = c(NA,
10L), class = "data.frame")

[williaml]

Sorry, is that meant to be df? It is still not reproducible. I get this error when I run it.

> pairs(df,
+       lower.panel=panel, upper.panel=panel.cor,diag.panel=panel.hist)
Error in pairs.default(df, lower.panel = panel, upper.panel = panel.cor,  : 
  non-numeric argument to 'pairs'