Update of MarkdownReports

Updated / new functions:
- substrRight
- setup_MarkdownReports
- md.LogSettingsFromList
- log_settings_MarkDown
- llwrite_list
- wlegend
- wLinRegression
- wscatter.fill

Development/Create_the_MarkdownReports_Package.R

@@ -42,7 +42,7 @@ DESCRIPTION <- list("Title" = "Generate Scientific Figures and Reports Easily",
     3. Link & display your figures automatically inside your report, right there where they are needed.
     4. Version your findings, annotating which parameters were used to reach certain results.
     5. Share your report with others via email, Github or a personal website.", "License" = "GNU GPL 3",
-		"Version"= "2.8", "Imports" = "vioplot, gplots, VennDiagram"
+		"Version"= "2.8.1", "Imports" = "vioplot, gplots, VennDiagram"
 )
 
 setwd(RepositoryDir)

MarkdownReports/R/MarkdownReports.R

@@ -488,20 +488,24 @@ wplot <-function (df_2columns, col = 1, pch = 18, ..., plotname = substitute(df_
 
 
 
-wscatter.fill <- function (x, y, ..., color, xlim=range(x), ylim=range(y), zlim=range(color),
-                           nlevels = 20, pch=21, cex=1,
-                           plotname = substitute(variable), plot.title = plotname, xlb = substitute(x), ylb = substitute(y),
+wscatter.fill <- function (df2col = cbind("A"=rnorm(100), "B"=rnorm(100)), ..., color, xlim=range(df2col[,1]), ylim=range(df2col[,2]), zlim=range(color), nlevels = 20, pch=21, cex=1,
+                           plotname = substitute(df2col), plot.title = plotname,
                            plot.axes, key.title, key.axes, asp = NA, xaxs = "i", yaxs = "i", las = 1,
-                           axes = TRUE, frame.plot = axes,
+                           axes = TRUE, frame.plot = axes, xlb, ylb,
                            savefile = T, w = 7, h = w, incrBottMarginBy = 0, mdlink = F ) {
+  x = df2col[,1]
+  y = df2col[,2]
+  CNN = colnames(df2col)
+  xlb = if(length(CNN) & missing(xlb)) CNN[1]
+  ylb = if(length(CNN) & missing(ylb)) CNN[2]
 
   fname = kollapse(plotname, ".barplot")
   if (incrBottMarginBy) { .ParMarDefault <- par("mar"); 	par(mar=c(par("mar")[1]+incrBottMarginBy, par("mar")[2:4]) ) } 	# Tune the margin
 
   mar.orig <- (par.orig <- par(c("mar", "las", "mfrow")))$mar
   on.exit(par(par.orig))
-  w <- (3 + mar.orig[2L]) * par("csi") * 2.54
-  layout(matrix(c(2, 1), ncol = 2L), widths = c(1, lcm(w)))
+  WID <- (3 + mar.orig[2L]) * par("csi") * 2.54
+  layout(matrix(c(2, 1), ncol = 2L), widths = c(1, lcm(WID)))
   par(las = las)
   mar <- mar.orig
   mar[4L] <- mar[2L]
@@ -526,8 +530,8 @@ wscatter.fill <- function (x, y, ..., color, xlim=range(x), ylim=range(y), zlim=
   par(mar = mar)
 
   # points
-  plot(x, y, main =plot.title, type = "n", xaxt='n', yaxt='n', ..., xlim=xlim, ylim=ylim, bty="n")
-  points(x, y, bg = colz, xaxt='n', yaxt='n', xlab="", ylab="", bty="n", pch=pch, ...)
+  plot(x, y, main =plot.title, type = "n", xaxt='n', yaxt='n', ..., xlim=xlim, ylim=ylim, bty="n", xlab=xlb, ylab=ylb)
+  points(x, y, bg = colz, xaxt='n', yaxt='n', xlab="", ylab="", bty="n", pch=pch,...)
 
   ## options to make mapping more customizable
   if (missing(plot.axes)) {

MarkdownReports/R/MarkdownReports.R.bac

@@ -488,20 +488,24 @@ wplot <-function (df_2columns, col = 1, pch = 18, ..., plotname = substitute(df_
 
 
 
-wscatter.fill <- function (x, y, ..., color, xlim=range(x), ylim=range(y), zlim=range(color),
-                           nlevels = 20, pch=21, cex=1,
-                           plotname = substitute(variable), plot.title = plotname, xlb = substitute(x), ylb = substitute(y),
+wscatter.fill <- function (df2col = cbind("A"=rnorm(100), "B"=rnorm(100)), ..., color, xlim=range(df2col[,1]), ylim=range(df2col[,2]), zlim=range(color), nlevels = 20, pch=21, cex=1,
+                           plotname = substitute(df2col), plot.title = plotname,
                            plot.axes, key.title, key.axes, asp = NA, xaxs = "i", yaxs = "i", las = 1,
-                           axes = TRUE, frame.plot = axes,
+                           axes = TRUE, frame.plot = axes, xlb, ylb,
                            savefile = T, w = 7, h = w, incrBottMarginBy = 0, mdlink = F ) {
+  x = df2col[,1]
+  y = df2col[,2]
+  CNN = colnames(df2col)
+  xlb = if(length(CNN) & missing(xlb)) CNN[1]
+  ylb = if(length(CNN) & missing(ylb)) CNN[2]
 
   fname = kollapse(plotname, ".barplot")
   if (incrBottMarginBy) { .ParMarDefault <- par("mar"); 	par(mar=c(par("mar")[1]+incrBottMarginBy, par("mar")[2:4]) ) } 	# Tune the margin
 
   mar.orig <- (par.orig <- par(c("mar", "las", "mfrow")))$mar
   on.exit(par(par.orig))
-  w <- (3 + mar.orig[2L]) * par("csi") * 2.54
-  layout(matrix(c(2, 1), ncol = 2L), widths = c(1, lcm(w)))
+  WID <- (3 + mar.orig[2L]) * par("csi") * 2.54
+  layout(matrix(c(2, 1), ncol = 2L), widths = c(1, lcm(WID)))
   par(las = las)
   mar <- mar.orig
   mar[4L] <- mar[2L]
@@ -526,8 +530,8 @@ wscatter.fill <- function (x, y, ..., color, xlim=range(x), ylim=range(y), zlim=
   par(mar = mar)
 
   # points
-  plot(x, y, main =plot.title, type = "n", xaxt='n', yaxt='n', ..., xlim=xlim, ylim=ylim, bty="n")
-  points(x, y, bg = colz, xaxt='n', yaxt='n', xlab="", ylab="", bty="n", pch=pch, ...)
+  plot(x, y, main =plot.title, type = "n", xaxt='n', yaxt='n', ..., xlim=xlim, ylim=ylim, bty="n", xlab=xlb, ylab=ylb)
+  points(x, y, bg = colz, xaxt='n', yaxt='n', xlab="", ylab="", bty="n", pch=pch,...)
 
   ## options to make mapping more customizable
   if (missing(plot.axes)) {