v0.3.6

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: vertesy/ggExpress - the fastest way to create, annotate and and save plots in R.
-version: v0.3.5
+version: v0.3.6
 message: >-
   If you use this software, please cite it using these metadata.
 type: software

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ggExpress
 Title: ggExpress is the fastest way to create, annotate and export plots
     in R
-Version: 0.3.5
+Version: 0.3.6
 Authors@R: 
     person("Abel", "Vertesy", , "[email protected]", role = c("aut", "cre"))
 Author: Abel Vertesy <[email protected]> [aut, cre]
@@ -38,6 +38,6 @@ Imports:
     stats,
     tidyverse
 Encoding: UTF-8
-Packaged: 2021-12-14 20:42:20
+Packaged: 2022-01-16 18:56:12
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.2

Development/Create_the_ggExpress_Package.v0.1.R

@@ -19,7 +19,7 @@ require('Stringendo')
 
 # Setup ------------------------
 PackageName = "ggExpress"
-package.version = "0.3.5"
+package.version = "0.3.6"
 setwd("~/GitHub/Packages/")
 
 RepositoryDir = kollapse("~/GitHub/Packages/", PackageName, "/")

Development/Development.bac

@@ -1,8 +1,8 @@
 # ____________________________________________________________________
 # ggExpress is the fastest way to create, annotate and export plots in R.  ----
 # ____________________________________________________________________
-# try(source("~/GitHub/Packages/ggExpress/R/ggExpress.functions.R"), silent = T)
-# try(source("https://raw.githubusercontent.com/vertesy/ggExpress/main/ggExpress.functions.R"), silent = T)
+# try(source("~/GitHub/Packages/ggExpress/R/ggExpress.R"), silent = T)
+# try(source("https://raw.githubusercontent.com/vertesy/ggExpress/main/ggExpress.R"), silent = T)
 
 # ______________________________________________________________________________________________----
 # Main plotting functions  ----
@@ -36,7 +36,7 @@
 #' @examples weight <- rnorm(1000); qhistogram(vec = weight); qhistogram(vec = weight, vline = 2, filtercol = -1)
 
 
-qhistogram <- function(vec, ext = "pdf", xlab = F, plot = TRUE, save = TRUE, mdlink = FALSE
+qhistogram <- function(vec, ext = "pdf", xlab = F, plot = TRUE, save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = F)
                        , suffix = NULL
                        , plotname = sppp(substitute(vec), suffix)
                        , logX = F, logY = F
@@ -102,7 +102,7 @@ qhistogram <- function(vec, ext = "pdf", xlab = F, plot = TRUE, save = TRUE, mdl
 qdensity <- function(vec, ext = "pdf", xlab = F, plot = TRUE
                      , suffix = NULL
                      , plotname = sppp(substitute(vec), suffix)
-                     , save = TRUE, mdlink = FALSE
+                     , save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = F)
                      , logX = F, logY = F
                      , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
                      , max.names = 50
@@ -161,7 +161,7 @@ qbarplot <- function(vec, ext = "pdf", plot = TRUE
                      , suffix = NULL
                      , plotname = sppp(substitute(vec), suffix)
                      # , title = F
-                     , save = TRUE, mdlink = FALSE
+                     , save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = F)
                      , hline = F, filtercol = 1
                      , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
                      , col = as.character(1:3)[1]
@@ -175,17 +175,19 @@ qbarplot <- function(vec, ext = "pdf", plot = TRUE
 
 
   if (isFALSE(xlab)) xlab = plotname
-  df <- qqqCovert.named.vec2tbl(namedVec = vec, thr = max.names)
+  df <- qqqCovert.named.vec2tbl(namedVec = vec, strip.too.many.names =F)
   # nrCategories.DFcol1 <- length(unique(df[,1])); stopif( nrCategories.DFcol1 >100)
 
   if (length(unique(df$"names")) == 1) df$"names" <- as.character(1:length(vec))
-  df[["colour"]] <- if (hline & filtercol != 0) {
-    if (filtercol == 1 ) (df$"value" > hline) else if (filtercol == -1 ) (df$"value" < hline)
-  } else if (length(col) == length(vec)) {
-    as.character(col)
-  } else {
-    as.character(rep(col, length(vec))[1:length(vec)])
-  }
+
+  df[["colour"]] <-
+    if (length(col) == length(vec)) {
+      as.character(col)
+    } else if (hline & filtercol != 0) {
+      if (filtercol == 1 ) (df$"value" > hline) else if (filtercol == -1 ) (df$"value" < hline)
+    } else {
+      as.character(rep(col, length(vec))[1:length(vec)])
+    }
   print(df)
 
   p <- ggpubr::ggbarplot(data = df, x = "names", y = "value"
@@ -195,6 +197,7 @@ qbarplot <- function(vec, ext = "pdf", plot = TRUE
                          , palette = palette_use, ...
   ) + ggpubr::grids(axis = 'y')
 
+  if (length(vec) > max.names) p <- p + ggplot2::guides(x = 'none')
   if (hide.legend) { p <- p + ggplot2::theme(legend.position = "none"
     , axis.text.x = ggplot2::element_text(angle = xlab.angle, hjust = 1) )
   }
@@ -238,7 +241,7 @@ qbarplot <- function(vec, ext = "pdf", plot = TRUE
 #' @examples xvec <- c("A"=12, "B"=29); qpie(vec = xvec)
 
 qpie <- function(vec = Network.Size
-                 , ext = "pdf", plot = TRUE, save = TRUE, mdlink = FALSE
+                 , ext = "pdf", plot = TRUE, save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = F)
                  , suffix = NULL
                  , plotname = sppp(substitute(vec), suffix)
                  , LegendSide = TRUE
@@ -247,8 +250,9 @@ qpie <- function(vec = Network.Size
                  , custom.order = FALSE
                  , extended.canvas = TRUE
                  , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
+                 , custom.margin = T
                  , max.categories = 100
-                 , max.names = 5
+                 , max.names = 10
                  , decr.order = TRUE
                  , both_pc_and_value = TRUE
                  , w = 5, h = w, ...) {
@@ -273,7 +277,7 @@ qpie <- function(vec = Network.Size
 
   if (is.null(names(vec))) { names(vec) <- as.character(1:length(vec)) }
 
-  df <- qqqCovert.named.vec2tbl.v2(namedVec = vec, thr = max.names)
+  df <- qqqCovert.named.vec2tbl(namedVec = vec, thr = max.names)
   if (l.orig > max.categories) df[['names']][length(df$'names')] <- name.of.last
 
   pcX <- df$"value" / sum(df$"value")
@@ -363,7 +367,7 @@ qboxplot <- function(df_XYcol
                      , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
                      , ext = "png", also.pdf = T
                      , logY = F #, logX = F
-                     , hline = F, vline = F, plot = TRUE, save = TRUE, mdlink = FALSE
+                     , hline = F, vline = F, plot = TRUE, save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = F)
                      , w = 7, h = w, ...) {
   # plotname <- if (isFALSE(title)) Stringendo::kpp(make.names(as.character(substitute(df_XYcol))), suffix) else title
   vars <- colnames(df_XYcol)
@@ -433,7 +437,7 @@ qviolin <- function(df_XYcol
                     , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
                     , ext = "png", also.pdf = T
                     , logY = F #, logX = F
-                    , hline = F, vline = F, plot = TRUE, save = TRUE, mdlink = FALSE
+                    , hline = F, vline = F, plot = TRUE, save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = F)
                     , w = 7, h = w, ...) {
   # plotname <- if (isFALSE(title)) Stringendo::kpp(make.names(as.character(substitute(df_XYcol))), suffix) else title
   vars <- colnames(df_XYcol)
@@ -493,7 +497,7 @@ qscatter <- function(df_XYcol
                      , palette_use = c("RdBu", "Dark2", "Set2", "jco", "npg", "aaas", "lancet", "ucscgb", "uchicago")[4]
                      , ext = "png", also.pdf = T
                      , logX = F, logY = F
-                     , hline = F, vline = F, plot = TRUE, save = TRUE, mdlink = FALSE
+                     , hline = F, vline = F, plot = TRUE, save = TRUE, mdlink = MarkdownHelpers::unless.specified('b.mdlink', def = F)
                      , w = 7, h = w, ...) {
   # plotname <- if (isFALSE(title)) Stringendo::kpp(make.names(as.character(substitute(df_XYcol))), suffix) else title
   vars <- colnames(df_XYcol)
@@ -608,13 +612,14 @@ qqqCovert.named.vec2tbl <- function(namedVec=1:14, verbose = F, strip.too.many.n
 
   # Check naming issues
   nr.uniq.names <- length(unique(names(namedVec)))
-  if (nr.uniq.names > thr & verbose)  print("Vector has", thr, "+ names. Can mess up auto-color legends.")
+  if (nr.uniq.names > thr & verbose)  iprint("Vector has", thr, "+ names. Can mess up auto-color legends.")
   if (nr.uniq.names < 1 & verbose) print("Vector has no names")
   an.issue.w.names <- (nr.uniq.names > thr | nr.uniq.names < 1 )
 
   idx.elements.above.thr <- if (thr < length(namedVec)) thr:length(namedVec) else 1:length(namedVec)
   if (strip.too.many.names & an.issue.w.names) names(namedVec)[idx.elements.above.thr] <- rep("", length(idx.elements.above.thr))
-  if (length(unique(names(namedVec))) > thr) print("Vector has", thr, "+ names. Can mess up auto-color legends.")
+
+  if (length(unique(names(namedVec))) > thr) iprint("Vector has", thr, "+ names. Can mess up auto-color legends.")
 
   df <- tibble::as_tibble(cbind("value" = namedVec))
   nm <- names(namedVec)