From 9806cd79ae70625fb968a9bf9ad49421ed925b59 Mon Sep 17 00:00:00 2001 From: vertesy Date: Fri, 26 Feb 2016 13:57:32 +0100 Subject: [PATCH] repo cleanup --- .../Create_the_MarkdownReports_Package.R | 0 .../MarkdownReports.R.annot.R | 0 .../MarkdownReports.Simple.R | 0 .../Old_versions}/MarkdownReports.01.zip | Bin .../Old_versions}/MarkdownReports.R.annot.zip | Bin .../Old_versions/MarkdownReports.unused.zip | Bin 0 -> 1503 bytes .../Old_versions/MarkdownReports.zip | Bin .../Usage_Example_Script.R | 0 .../Usage_Example_Script}/DreamMap.plot.pdf | Bin .../Usage_Example_Script}/DreamMap.plot.png | Bin .../Usage_Example_Script.R.log.backup.zip | Bin .../Usage_Example_Script.R.log.md | 0 .../Data.hist.pdf | Bin .../DreamMap.plot.pdf | Bin .../Usage_Example_Script.R.log.md | 0 .../Usage_Example_Script}/data.hist.pdf | Bin .../Usage_Example_Script}/data.hist.png | Bin MarkdownReports.unused.R | 74 -- MarkdownReports/R/MarkdownReports.R.bac | 1024 ----------------- 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b/Development/Old_versions/MarkdownReports.R.annot.zip similarity index 100% rename from Old_versions/MarkdownReports.R.annot.zip rename to Development/Old_versions/MarkdownReports.R.annot.zip diff --git a/Development/Old_versions/MarkdownReports.unused.zip b/Development/Old_versions/MarkdownReports.unused.zip new file mode 100644 index 0000000000000000000000000000000000000000..5e1858b2e7d8651b335e2ad232b43ba9bd797993 GIT binary patch literal 1503 zcmZ|PYdF&j90&0KW)|BL(l(Ub3PKLxegUlTP_WqI*!hHcb=!`_u~6|^Zma3I6F!~lmGyb0gi{d;Xib|UQm_> z03`(gKm$7gB847&iWVD2qK4DxQIVMFu;@tYDGcd^t1KX8QPWS3=k}AMG4&$$@+>$3Li7uHx`4Bb{h!6T^(wGQd*4*}U5e~EM* zS$XFDjZv?=z7=L^#;=Z#$4=IbCg)FDqmD2uBe-l3S6Jy#tJNnQ#v3Z$D;5UE=z&`T zT3-%5${9u6+UDI8zY2^eJ`{A`hTx1tTZ(nm_*%1pb4gz*7S-OI^~(AAS8sw;1g8?B z54m%fH-@snU?gf7eNn#K>0uTrl zFhB1-;+y9)jdu*?EUc8kje(w@$mvPjcx^Ndc0!)U%w}e0f;vSPJl)WY29@fTP;2-D zEkkpr>r2o`vf&n8>d{W3(=rfeGpSHbliNL0o}yTfBw z?|kW)tXm(A3`^CU-dOnFZWNlZ!a-ddew^cq6xvyuC9{=;=V2PRG%vX`?HkY;%WrDU 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pdf image, in inches. -#' @param plotname The name of the file. -#' @param breaks Number of bins. -#' @param main Title of the plot. -#' @param xlb X-axis label. -#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF". -#' @param h Height of the saved pdf image, in inches.line -#' @param vline Draw a vertical line at the value you pass on to it. Useful to display a threshold. Design the line by "lty", "lwd" & "lcol" parameters. -#' @param lty Linetype, defined by numbers 1-6. -#' @param lwd Line width. Set to 2 by default. -#' @param lcol Color of the line. -#' @param filtercol Color bars below / above the threshold with red / green. Define the direction by -1 or 1. Takes effect if "vline" is defined. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @examples whist (variable = , col = gold1, w = 7, h = 7, plotname = substitute(variable), breaks = 20, main = kollapse("Histogram of ", substitute(variable)), xlb = substitute(variable), mdlink = FALSE, hline = F, vline = F, lty = 2, lwd = 3, lcol = 2, filtercol = 0, ... = ) -#' @export - -whist <-function (variable, col = "gold1", w = 7, h = 7, plotname = substitute(variable), breaks = 20, main = kollapse("Histogram of ", substitute(variable)), xlb = substitute(variable), mdlink = FALSE, hline = F, - vline = F, lty = 2, lwd = 3, lcol = 2, filtercol = 0, ...) -{ - xtra = list(...) - if (length(variable) > 0) { - fname = kollapse(plotname, ".hist") - if (!is.numeric(variable)) { - variable = table(variable) - cexNsize = 0.7/abs(log10(length(variable))) - cexNsize = min(cexNsize, 1) - barplot(variable, ..., main = main, xlab = xlb, col = col, las = 2, cex.names = cexNsize, - sub = paste("mean:", iround(mean(variable, na.rm = T)), "CV:", percentage_formatter(cv(variable)))) - } - else { - histdata = hist(variable, breaks = breaks, plot = F) - if (filtercol == 1) { - col = (histdata$breaks >= vline) + 2 - } - else if (filtercol == -1) { - col = (histdata$breaks < vline) + 2 - } - hist(variable, ..., main = main, breaks = breaks, xlab = xlb, col = col, las = 2) - } - if (hline) { - abline(h = hline, lty = lty, lwd = lwd, col = lcol) - } - if (vline & !l(xtra$xlim)) { - PozOfvline = mean(histdata$mids[c(max(which(histdata$breaks < vline)), min(which(histdata$breaks >= - vline)))]) - abline(v = PozOfvline, lty = lty, lwd = lwd, col = 1) - } - else if (vline & l(xtra$xlim)) { - abline(v = vline, lty = lty, lwd = lwd, col = 1) - } - dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h) - } - else { - any_print(variable, " IS EMPTY") - } - assign("plotnameLastPlot", fname, envir = .GlobalEnv) - if (mdlink) { - MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname) - } -} - - -#' wbarplot -#' -#' Create and save bar plots as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions. -#' @param variable The variable to plot. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @param col Color of the plot. -#' @param sub Subtitle for the plot. -#' @param plotname The name of the file saved. -#' @param main The title of the plot. -#' @param w Width of the saved pdf image, in inches. -#' @param h Height of the saved pdf image, in inches. -#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot. -#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF". -#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels. -#' @param hline Draw a horizontal line at the value you pass on to it. Useful to display a threshold. Design the line by "lty", "lwd" & "lcol" parameters. -#' @param vline Draw a vertical line at the value you pass on to it. Useful to display a threshold. Design the line by "lty", "lwd" & "lcol" parameters. -#' @param filtercol Color bars below / above the threshold with red / green. Define the direction by -1 or 1. Takes effect if "hline" is defined. -#' @param lty Linetype, defined by numbers 1-6. -#' @param lwd Line width. Set to 2 by default. -#' @param lcol Color of the line. -#' @param errorbar Draw error bars if TRUE. Pass on the value in parameters "upper" and "lower". Refine the look by "w" and "arrow_lwd". -#' @param upper Size of the upper error bar. -#' @param lower Size of the lower error bar. By default, it equals the upper error bar. -#' @param w Width of the saved pdf image, in inches.idth -#' @param arrow_lwd Line width for the error bar arrow. -#' @examples wbarplot (variable = , ... = , col = gold1, sub = F, plotname = substitute(variable), main = substitute(variable), w = 7, h = 7, incrBottMarginBy = 0, mdlink = F, tilted_text = F, hline = F, vline = F, filtercol = 1, lty = 1, lwd = 2, lcol = 2, errorbar = F, upper = 0, lower = upper, width = 0.1, arrow_lwd = 1) -#' @export - -wbarplot <-function (variable, ..., col = "gold1", sub = F, plotname = substitute(variable), main = substitute(variable), w = 7, h = 7, incrBottMarginBy = 0, mdlink = F, tilted_text = F, hline = F, vline = F, filtercol = 1, - lty = 1, lwd = 2, lcol = 2, errorbar = F, upper = 0, lower = upper, width = 0.1, arrow_lwd = 1) -{ - fname = kollapse(plotname, ".barplot") - .ParMarDefault <- par("mar") - par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4])) - cexNsize = 0.8/abs(log10(length(variable))) - cexNsize = min(cexNsize, 1) - if (sub == T) { - subtitle = paste("mean:", iround(mean(variable, na.rm = T)), "CV:", percentage_formatter(cv(variable))) - } - else if (sub == F) { - subtitle = "" - } - else { - subtitle = sub - } - if (hline & filtercol == 1) { - col = (variable >= hline) + 2 - } - if (hline & filtercol == -1) { - col = (variable < hline) + 2 - } - if (errorbar) { - ylim = range(c(0, (variable + upper + abs(0.1 * variable)), variable - lower - abs(0.1 * variable)), - na.rm = T) - } - else { - ylim = range(0, variable) - } - if (tilted_text) { - xlb = NA - } - else { - xlb = names(variable) - } - x = barplot(variable, ..., names.arg = xlb, main = main, sub = subtitle, col = col, las = 2, cex.names = cexNsize, - ylim = ylim) - if (hline) { - abline(h = hline, lty = lty, lwd = lwd, col = lcol) - } - if (vline) { - abline(v = vline, lty = lty, lwd = lwd, col = lcol) - } - if (errorbar) { - arrows(x, variable + upper, x, variable - lower, angle = 90, code = 3, length = width, lwd = arrow_lwd, - ...) - } - if (tilted_text) { - text(x = x - 0.25, y = -max(nchar(names(variable)))/5, labels = names(variable), xpd = TRUE, - srt = 45, cex = cexNsize) - } - dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h) - par(mar = .ParMarDefault) - assign("plotnameLastPlot", fname, envir = .GlobalEnv) - if (mdlink) { - MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname) - } -} - - -#' wboxplot -#' -#' Create and save box plots as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions. -#' @param variable The variable to plot. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @param col Color of the plot. -#' @param plotname Title of the plot (main parameter) and also the name of the file. -#' @param sub Subtitle for the plot. -#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot. -#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels. -#' @param w Width of the saved pdf image, in inches. -#' @param h Height of the saved pdf image, in inches. -#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF". -#' @examples wboxplot (variable = , ... = , col = gold1, plotname = as.character(substitute(variable)), sub = FALSE, incrBottMarginBy = 0, tilted_text = F, w = 7, h = 7, mdlink = F) -#' @export - -wboxplot <-function (variable, ..., col = "gold1", plotname = as.character(substitute(variable)), sub = FALSE, incrBottMarginBy = 0, tilted_text = F, w = 7, h = 7, mdlink = F) -{ - fname = kollapse(plotname, ".boxplot") - .ParMarDefault <- par("mar") - par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4])) - if (tilted_text) { - xlb = NA - } - else { - xlb = names(variable) - } - boxplot(variable, ..., names = xlb, main = plotname, col = col, las = 2) - if (tilted_text) { - text(x = 1:l(variable), y = -max(nchar(names(variable)))/2, labels = names(variable), xpd = TRUE, - srt = 45) - } - dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h) - assign("plotnameLastPlot", fname, envir = .GlobalEnv) - par(mar = .ParMarDefault) - if (mdlink) { - MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname) - } -} - - -#' wpie -#' -#' Create and save pie charts as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions. -#' @param variable The variable to plot. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @param percentage Display percentage instead of counts. TRUE by default. -#' @param plotname Title of the plot (main parameter) and also the name of the file. -#' @param w Width of the saved pdf image, in inches. -#' @param h Height of the saved pdf image, in inches. -#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF". -#' @examples wpie (variable = , ... = , percentage = TRUE, plotname = substitute(variable), w = 7, h = 7, mdlink = F) -#' @export - -wpie <-function (variable, ..., percentage = TRUE, plotname = substitute(variable), w = 7, h = 7, mdlink = F) { - fname = kollapse(plotname, ".pie") - subt = kollapse("Total = ", sum(variable), print = F) - if (percentage) { - labs <- paste("(", names(variable), ")", "\n", percentage_formatter(variable/sum(variable)), - sep = "") - } - else { - labs <- paste("(", names(variable), ")", "\n", variable, sep = "") - } - pie(variable, ..., main = plotname, sub = subt, clockwise = T, labels = labs, col = rainbow(l(variable))) - dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h) - if (mdlink) { - MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname) - } -} - - -#' wstripchart -#' -#' Create and save strip charts as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions. -#' @param yalist Input list to be plotted. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @param plotname Title of the plot (main parameter) and also the name of the file. -#' @param sub Subtitle for the plot. -#' @param border An optional vector of colors for the outlines of the boxplots. The values in border are recycled if the length of border is less than the number of plots. -#' @param BoxPlotWithMean Display the mean instead of the median in a boxplot. This is non-standard use of a boxplot, report it. -#' @param pch Define the symbol for each data point. A number [0-25] or any string between ""-s. -#' @param pchlwd Define the outline width of the symbol for each data point. -#' @param pchcex Define the size of the symbol for each data point. -#' @param bg Background color. -#' @param col Color of the plot. -#' @param metod Method for displaying data points to avoid overlap; either"jitter" or "stack". See stripchart(). -#' @param jitter The amount of horizontal scatter added to the individual data points (to avoid overlaps). -#' @param col Color of the plot.orbyColumn -#' @param w Width of the saved pdf image, in inches. -#' @param h Height of the saved pdf image, in inches. -#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot. -#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels. -#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF". -#' @examples wstripchart (yalist = , ... = , plotname = as.character(substitute(yalist)), sub = FALSE, border = 1, BoxPlotWithMean = F, pch = 23, pchlwd = 1, pchcex = 1.5, bg = chartreuse2, col = black, metod = jitter, jitter = 0.2, colorbyColumn = F, w = 7, h = 7, incrBottMarginBy = 0, tilted_text = F, mdlink = F) -#' @export - -wstripchart <-function (yalist, ..., plotname = as.character(substitute(yalist)), sub = FALSE, border = 1, BoxPlotWithMean = F, pch = 23, pchlwd = 1, pchcex = 1.5, bg = "chartreuse2", col = "black", metod = "jitter", jitter = 0.2, - colorbyColumn = F, w = 7, h = 7, incrBottMarginBy = 0, tilted_text = F, mdlink = F) -{ - .ParMarDefault <- par("mar") - par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4])) - cexNsize = 1/abs(log10(length(yalist))) - cexNsize = min(cexNsize, 1) - fname = kollapse(plotname, ".stripchart") - a = boxplot(yalist, plot = F) - if (colorbyColumn) { - pchlwd = 5 - pchcex = 0.5 - } - if (BoxPlotWithMean) { - a$stats[3, ] = unlist(lapply(yalist, mean)) - } - if (tilted_text) { - xlb = F - } - else { - xlb = T - } - bxp(a, xlab = "", show.names = xlb, ..., main = plotname, border = border, outpch = NA, las = 2, - outline = T, cex.axis = cexNsize) - stripchart(yalist, vertical = TRUE, add = TRUE, method = metod, jitter = jitter, pch = pch, bg = bg, - col = col, lwd = pchlwd, cex = pchcex) - if (tilted_text) { - text(x = 1:l(yalist), y = -max(nchar(names(yalist)))/2, labels = names(yalist), xpd = TRUE, srt = 45) - } - dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h) - par(mar = .ParMarDefault) - assign("plotnameLastPlot", fname, envir = .GlobalEnv) - if (mdlink) { - MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname) - } -} - - -#' wstripchart_list -#' -#' Create and save stripcharts from a list as .pdf, in "OutDir". This version allows individual coloring of each data point, by a color-list of the same dimension. If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions. -#' @param yalist Input list to be plotted. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @param plotname Title of the plot (main parameter) and also the name of the file. -#' @param sub Subtitle for the plot. -#' @param ylb Y-axis label. -#' @param xlb X-axis label. -#' @param border An optional vector of colors for the outlines of the boxplots. The values in border are recycled if the length of border is less than the number of plots. -#' @param bxpcol Color of the boxplot outlines. -#' @param pch Define the symbol for each data point. A number [0-25] or any string between ""-s. -#' @param pchlwd Define the outline width of the symbol for each data point. -#' @param pchcex Define the size of the symbol for each data point. -#' @param bg Background color. -#' @param col Color of the plot.l -#' @param metod Method for displaying data points to avoid overlap; either"jitter" or "stack". See stripchart(). -#' @param jitter The amount of horizontal scatter added to the individual data points (to avoid overlaps). -#' @param w Width of the saved pdf image, in inches. -#' @param h Height of the saved pdf image, in inches. -#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot. -#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels. -#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF". -#' @examples wstripchart_list (yalist = , ... = , plotname = as.character(substitute(yalist)), sub = FALSE, ylb = NULL, xlab = NULL, border = 1, bxpcol = 0, pch = 23, pchlwd = 1, pchcex = 1.5, bg = chartreuse2, coll = black, metod = jitter, jitter = 0.2, w = 7, h = 7, incrBottMarginBy = 0, tilted_text = F, mdlink = F) -#' @export - -wstripchart_list <-function (yalist, ..., plotname = as.character(substitute(yalist)), sub = FALSE, ylb = "NULL", xlab = "NULL", border = 1, bxpcol = 0, pch = 23, pchlwd = 1, pchcex = 1.5, bg = "chartreuse2", coll = "black", metod = "jitter", - jitter = 0.2, w = 7, h = 7, incrBottMarginBy = 0, tilted_text = F, mdlink = F) -{ - fname = kollapse(plotname, ".stripchart") - .ParMarDefault <- par("mar") - par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4])) - cexNsize = 1/abs(log10(length(list))) - cexNsize = min(cexNsize, 1) - if (tilted_text) { - xlb = F - } - else { - xlb = T - } - boxplot(yalist, ..., show.names = xlb, main = plotname, border = border, outline = FALSE, las = 2, - col = bxpcol, cex.axis = cexNsize) - for (i in 1:length(yalist)) { - j = k = i - if (length(coll) < length(yalist)) { - j = 1 - } - if (length(bg) < length(yalist)) { - k = 1 - } - stripchart(na.omit(yalist[[i]]), at = i, add = T, vertical = T, method = metod, jitter = jitter, - pch = pch, bg = bg[[k]], col = coll[[j]], lwd = pchlwd, cex = pchcex) - } - if (tilted_text) { - text(x = 1:l(yalist), y = -max(nchar(names(yalist)))/2, labels = names(yalist), xpd = TRUE, srt = 45) - } - dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h) - par(mar = .ParMarDefault) - assign("plotnameLastPlot", fname, envir = .GlobalEnv) - if (mdlink) { - MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname) - } -} - - -#' wvioplot_list -#' -#' Create and save violin plots as .pdf, in "OutDir". It requires (and calls) "vioplot" package. If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions. -#' @param yalist Input list to be plotted. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @param xlb X-axis label. -#' @param ylb Y-axis label. -#' @param col Color of the plot.l -#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot. -#' @param w Width of the saved pdf image, in inches. -#' @param h Height of the saved pdf image, in inches. -#' @param plotname Title of the plot (main parameter) and also the name of the file. -#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels. -#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF". -#' @examples wvioplot_list (yalist = , ... = , xlb = names(yalist), ylb = , coll = c(1:length(yalist)), incrBottMarginBy = 0, w = 7, h = 7, plotname = as.character(substitute(yalist)), tilted_text = F, mdlink = F) -#' @export - -wvioplot_list <-function (yalist, ..., xlb = names(yalist), ylb = "", coll = c(1:length(yalist)), incrBottMarginBy = 0, w = 7, h = 7, plotname = as.character(substitute(yalist)), tilted_text = F, mdlink = F) -{ - require(vioplot) - .ParMarDefault <- par("mar") - par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4])) - l_list = length(yalist) - fname = kollapse(plotname, ".vioplot") - if (length(coll) < l_list) { - coll = rep(coll, l_list) - } - if (tilted_text) { - xlb = NA - } - else { - xlb = names(yalist) - } - plot(0, 0, type = "n", xlim = c(0.5, (l_list + 0.5)), ylim = range(unlist(yalist)), xaxt = "n", xlab = "", - ylab = ylb, main = plotname) - for (i in 1:l_list) { - vioplot(na.omit(yalist[[i]]), ..., at = i, add = T, col = coll[i]) - } - axis(side = 1, at = 1:l_list, labels = xlb, las = 2) - if (tilted_text) { - text(x = 1:l(yalist), y = -max(nchar(names(yalist)))/2, labels = names(yalist), xpd = TRUE, srt = 45) - } - dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h) - par(mar = .ParMarDefault) - assign("plotnameLastPlot", fname, envir = .GlobalEnv) - if (mdlink) { - MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname) - } -} - - -#' wviostripchart_list -#' -#' Create and save violin plots as .pdf, in "OutDir". It requires (and calls) "vioplot" package. If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions. -#' @param yalist Input list to be plotted. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @param pch Define the symbol for each data point. A number [0-25] or any string between ""-s. -#' @param viocoll Background color of each individual violing plot. -#' @param vioborder Border color of each individual violing plot. -#' @param ylb Y-axis label. -#' @param plotname Title of the plot (main parameter) and also the name of the file. -#' @param sub Subtitle for the plot. -#' @param bg Background color. -#' @param col Color of the plot.l -#' @param metod Method for displaying data points to avoid overlap; either"jitter" or "stack". See stripchart(). -#' @param jitter The amount of horizontal scatter added to the individual data points (to avoid overlaps). -#' @param w Width of the saved pdf image, in inches. -#' @param h Height of the saved pdf image, in inches. -#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot. -#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF". -#' @examples wviostripchart_list (yalist = , ... = , pch = 23, viocoll = 0, vioborder = 1, ylb = , plotname = as.character(substitute(yalist)), sub = F, bg = 0, coll = black, metod = jitter, jitter = 0.1, w = 7, h = 7, incrBottMarginBy = 0, mdlink = F) -#' @export - -wviostripchart_list <-function (yalist, ..., pch = 23, viocoll = 0, vioborder = 1, ylb = "", plotname = as.character(substitute(yalist)), sub = F, bg = 0, coll = "black", metod = "jitter", jitter = 0.1, w = 7, h = 7, incrBottMarginBy = 0, - mdlink = F) -{ - fname = kollapse(plotname, ".VioStripchart") - require(vioplot) - .ParMarDefault <- par("mar") - par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4])) - l_list = length(yalist) - plot(0, 0, type = "n", xlim = c(0.5, (l_list + 0.5)), ylim = range(unlist(yalist)), xaxt = "n", xlab = "", - ylab = ylb, main = plotname) - for (i in 1:l_list) { - vioplot(na.omit(yalist[[i]]), ..., at = i, add = T, col = viocoll[i], border = vioborder[i]) - } - for (i in 1:length(yalist)) { - j = k = i - if (length(coll) < length(yalist)) { - j = 1 - } - if (length(bg) < length(yalist)) { - k = 1 - } - stripchart(na.omit(yalist[[i]]), at = i, add = T, vertical = T, method = metod, jitter = jitter, - pch = pch, bg = bg[[k]], col = coll[[j]]) - } - dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h) - par(mar = .ParMarDefault) - assign("plotnameLastPlot", fname, envir = .GlobalEnv) - if (mdlink) { - MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname) - } -} - - -#' whist_dfCol -#' -#' Use this version of whist() if you iterate over columns or rows of a data frame. You can name the file by naming the variable. Cannot be used with dynamically called variables [e.g. call vectors within a loop] -#' @param df Input data frame to be plotted -#' @param col Color of the plot.Name -#' @param col Color of the plot. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @param w Width of the saved pdf image, in inches. -#' @param h Height of the saved pdf image, in inches. -#' @examples whist_dfCol (df = , colName = , col = gold, ... = , w = 7, h = 7) -#' @export - -whist_dfCol <-function (df, colName, col = "gold", ..., w = 7, h = 7) { - stopifnot(colName %in% colnames(df)) - variable = unlist(df[, colName]) - stopifnot(length(variable) > 1) - plotname = paste(substitute(df), "__", colName, sep = "") - FullPath = FnP_parser(plotname, "hist.pdf") - if (!is.numeric(variable)) { - variable = table(variable) - cexNsize = 0.7/abs(log10(length(variable))) - cexNsize = min(cexNsize, 1) - barplot(variable, ..., main = plotname, col = col, las = 2, cex.names = cexNsize, sub = paste("mean:", - iround(mean(variable, na.rm = T)), "CV:", percentage_formatter(cv(variable)))) - } - else { - zz = hist(variable, ..., plot = F) - hist(variable, ..., main = plotname, col = col, las = 2, sub = paste("mean:", iround(mean(zz$counts)), - "median:", iround(median(zz$counts)))) - } - dev.copy2pdf(file = FullPath, width = w, height = h) -} - - -#' wbarplot_dfCol -#' -#' wbarplot for a column of a data frame. -#' @param df Input data frame to be plotted -#' @param col Color of the plot.Name -#' @param col Color of the plot. -#' @param w Width of the saved pdf image, in inches. -#' @param h Height of the saved pdf image, in inches. -#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work). -#' @examples wbarplot_dfCol (df = , colName = , col = gold1, w = 7, h = 7, ... = ) -#' @export - -wbarplot_dfCol <-function (df, colName, col = "gold1", w = 7, h = 7, ...) { - stopifnot(colName %in% colnames(df)) - variable = unlist(df[, colName]) - stopifnot(length(variable) > 1) - plotname = paste(substitute(df), "__", colName, sep = "") - FullPath = FnP_parser(plotname, "barplot.pdf") - cexNsize = 0.7/abs(log10(length(variable))) - cexNsize = min(cexNsize, 1) - barplot(variable, ..., main = plotname, col = col, las = 2, cex.names = cexNsize, sub = paste("mean:", - iround(mean(variable, na.rm = T)), "CV:", percentage_formatter(cv(variable)))) - dev.copy2pdf(file = FullPath, width = w, height = h) -} - - -#' val2col -#' -#' This function converts a vector of values("yourdata") to a vector of color levels. One must define the number of colors. The limits of the color scale("zlim") or the break points for the color changes("breaks") can also be defined. when breaks and zlim are defined, breaks overrides zlim. Source: http://menugget.blogspot.nl/2011/09/converting-values-to-color-levels.html -#' @param yourdata The data, to what the colors will be scaled to. -#' @param zlim Limits. -#' @param col Color of the plot. -#' @param breaks Number of bins. -#' @examples val2col (yourdata = , zlim = , col = rev(heat.colors(12)), breaks = ) -#' @export - -val2col <-function (yourdata, zlim, col = rev(heat.colors(12)), breaks) { - if (!missing(breaks)) { - if (length(breaks) != (length(col) + 1)) { - stop("must have one more break than color") - } - } - if (missing(breaks) & !missing(zlim)) { - breaks <- seq(zlim[1], zlim[2], length.out = (length(col) + 1)) - } - if (missing(breaks) & missing(zlim)) { - zlim <- range(yourdata, na.rm = TRUE) - zlim[2] <- zlim[2] + c(zlim[2] - zlim[1]) * (0.001) - zlim[1] <- zlim[1] - c(zlim[2] - zlim[1]) * (0.001) - breaks <- seq(zlim[1], zlim[2], length.out = (length(col) + 1)) - } - colorlevels <- col[((as.vector(yourdata) - breaks[1])/(range(breaks)[2] - range(breaks)[1])) * (length(breaks) - - 1) + 1] - colorlevels -} - - -#' error.bar -#' -#' Put error bars on top of your bar plots. This functionality is now integrated into MarkdownReporter's wbarplot() function -#' @param x X-position on the plot. -#' @param y Y-position on the plot. -#' @param upper Size of the upper error bar. -#' @param lower Size of the lower error bar. By default, it equals the upper error bar. -#' @param width Width of the erro bar whisker. -#' @param ... Pass any other parameter of the corresponding arrows function (most of them should work). -#' @examples error.bar (x = , y = , upper = , lower = upper, width = 0.1, ... = ) -#' @export - -error.bar <-function (x, y, upper, lower = upper, width = 0.1, ...) { - stopifnot(length(x) == length(y) & length(y) == length(lower) & length(lower) == length(upper)) - if (l(dim(y)) > 1) { - arrows(as.vector(x), as.vector(y + upper), as.vector(x), as.vector(y - lower), angle = 90, code = 3, - length = width , ...) - } - else { - arrows(x, y + upper, x, y - lower, angle = 90, code = 3, length = width , ...) - } -} - - -#' barplot.label -#' -#' Add extra labels to your bar plots at the top or the base. -#' @param x X-position of the label. -#' @param y Y-position of the label. -#' @param labels Label text. -#' @param bottom Put labels at the bottom of the bars. -#' @param relpos_top Relative offset. -#' @param relpos_bottom Relative offset. -#' @param ... 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-[*edit the website*](https://github.com/vertesy/MarkDownLogs/generated_pages/new) \ No newline at end of file diff --git a/Supplementary/Wiki.md b/Supplementary/Wiki.md deleted file mode 100644 index 03f8cc0..0000000 --- a/Supplementary/Wiki.md +++ /dev/null @@ -1,51 +0,0 @@ -# Functions of the MarkDownLogger library -...and some explanation... - -## Auxiliary functions - -1. ***kollapse*** - - parses (and prints) flexibly anything you pass on to it into a string -- ***any_print*** - - more flexible printing fun -- ***iround*** -- ***percentage_formatter*** - -## Setup Logging - -1. ***create_set_OutDir*** - - # Defines and creates the Output / Reports directory, with a timestamped subfolder where you can backup manually. -- ***setup_logging_markdown*** - - setup_logging file, path and modification date -- ***continue_logging_markdown*** - - continue writing to an existing markdown file - -## Write into your markdown log file - -1. ***log_settings_MarkDown*** - - log your parameter settings into a tabular format -- ***llprint*** - - log to markdown file and print to screen -- ***llogit*** - - log to markdown file, do not print -- ***MarkDown_ImgLink_formatter*** - - insert a link to a pdf image -- ***MarkDown_Img_Logger_PDF_and_PNG*** - - insert 2 links, one for PDF, one for PNG version of the same image (png files are needed for web or email sharing!!!) -- ***MarkDown_Img_Logger_4GitHub*** - - insert 2 links, one for PDF, one for PNG version of the same image (png files are needed for web or email sharing!!!) - -## Write out pretty tables to your markdown file - -1. ***MarkDown_Table_writer_DF_RowColNames*** -- ***MarkDown_Table_writer_NamedVector*** - -## Generate and save plots into pdf and insert a diplay-link into your markdown file -*All of them are based on the rfunction with the same name (without w prefix)* - -1. ***wplot*** -- ***whist*** -- ***wbarplot*** -- ***wboxplot*** -- ***wpie*** -- ***wplot_save_this*** - - This in a specific function: It saves the plot you created from the active device (in a pdf, with a link in the report if specified - as for all the above plotting functions). \ No newline at end of file