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Introduction to GrapheR

1. jpg png and tiff are available and the image length in pixels Image height is automatically calculated from the length value Figure 8 Finally click on the Save button 4 6 Changing the user language To change the user language click on the lang button of the navigation bar A dialog box opens on the right of the interface Figure 9 Choose the desired language in the drop down menu To fix your preference in the future tick the Save the preference checkbox Click on the Ok button to validate The interface is closed and re opened in the chosen language but note that any Size of African swallow Figure 8 Saving a graph dataset loaded in the previous language session is lost and has to be re loaded Language English X Al Save the preference V Ok Close Al Figure 9 Changing the user language 5 Implementing GrapheR in a new language Implementing GrapheR in another language is very easy because no word ap pearing in the interface is written in the code The button names etc come from an external file which is loaded depending on the language setting En glish French German and Spanish are available so far files Language en csv Language_fr csv Language_de csv and Language_es csv respectively in the lang directory of the package Therefore adding a new language just requires a strict translation of each line of one of the existing files including spaces before and or after words The
2. view The interface is divided into three blocks Fig 1 1 the navigation bar it contains all buttons opening the modules of the interface 2 the messages frame to make the interface using easier information mes sages are displayed in this frame when the mouse is over some specific elements or when some specific actions are performed 3 the settings block it contains all dialog boxes allowing to set the graph to be drawn Start by loading the dataset Loading the dataset External file Extension txt v Swallows Column separator space tabulation X Decimal separator point r Code for missing values NA Variables name indicated in the file IV Load Information about the dataset Rename variables Transform variables into factors Re order levels of a factor Figure 1 User interface global view display under Windows 7 3 2 Navigation bar The navigation bar is divided into seven groups of buttons each corresponding to one obligatory or optional step of the process Fig 2 ae SUE H ES 1 2 3 4 5 Yi 6 Figure 2 Navigation bar 1 loading and modifying the dataset 2 setting up a graph From left to right histogram box and whisker plot bar plot pie chart curve and scatter plot 3 opening a new graphics device when a graph is drawn it is in the active window or in a new device if none is open This button allows the user to open a new graphics device in which
3. Introduction to GrapheR Maxime Herv For any question comment or suggestion mx herve gmail com Thanks to Juan Alberti for the Spanish translation of the interface Thanks to Helmut Schlumprecht for the German translation of the interface and the user manual 1 Introduction GrapheR is a multiplatform Linux Mac OS Windows user interface for draw ing highly customizable graphs in R It aims to be a valuable help to quickly draw publishable graphs without knowing any R commands Six kinds of graph are available e histogram e box and whisker plot bar plot e pie chart e curve e scatter plot GrapheR was built on the tcltk package and consequently bugs can hap pen if R is configured in the MDI Multiple Document Interface mode It is recommended to configure it in SDI Single Document Interface mode before starting the package GrapheR needs to function at least the 2 10 version of R and one additional package tcltk Under Mac OS X Tcl Tk must have already been installed for more information see here 2 Launching the interface As with any other package GrapheR is loaded via library GrapheR require GrapheR or the Packages menu of the Windows R GUI At this time the tcltk package is automatically loaded Launching the interface is the only step that requires the user to enter a command run GrapheR The interface opens and the console can now be reduced 3 Description of the interface 3 1 Global
4. e dataset The first sub block Figure 3 allows you to load the dataset Data can be imported from an external file txt and csv extensions are available so far or can be an already existing R object of class data frame i e a table The next sub block allows you to get information on the dataset structure When a variable is selected in the list on the left its type numeric factor logical and its summary are displayed in the frame on the right The two next sub blocks allow the dataset to be modified if needed e by renaming variables for example if the dataset does not contain their names e by converting variables into factors The conversion can be applied to variables of class character i e characters chains vectors or to numeric variables in this case values can be grouped into classes The latter case is necessary when a factor is numerically coded e g a binary factors 0 1 otherwise R would treat it as a numeric variable 4 2 Setting up a graph Once the dataset is ready click on the button corresponding to the type of graph to be drawn histogram box and whisker plot bar plot pie chart curve or scatter plot Whatever the type of graph chosen all parameters have a default value except general parameters which correspond to variable s to be represented Hence to quickly draw a graph only general parameters must be defined If they are not or not all defined an error occurs when trying to draw the g
5. les name indicated in the file Saeed Information about the dataset Dataset variables Variable summary African 60 European 60 Rename variables Transform variables into factors Dataset variables Species ea No grouping 0 levels a itom Size Grouping by classes eight iii of same length C nce ofsamesize Re order levels of a factor Actual order New order Factor Re order Figure 3 Loading the dataset number of graphs to be drawn in the device to be created and the background color of this device Figure 5 It is possible to draw up to 16 graphs in the same device shared between four rows and four columns However the larger the number of graphs to be drawn the smaller the space allocated to each Warning only densities type allows to draw the distribution curve of the data General parameters Variable to be represented Factor optional Factor level Title Size of African swallow Subtitle Tiie Lower limt Auto Upper limit Auto Number of bars Auto _Distribution curve of data coor a a lie ja ie Figure 5 Opening a new graphics device 4 4 Adding elements to the graph Once the graph is drawn elements can be added to complete it e one or several horizontal line s e one or several vertical line s any other kind of line s e one or several theoretical distribution curve s only o
6. n density histograms e text e p values only on bar plots These elements are always added to the last graph drawn For each element clicking on the corresponding button in the navigation bar opens a dialog box on the right of the interface Here we want to add a distribution curve to the histogram corresponding to the values of a normal law of parameters 15 8 and o 2 2 parameters calculated from the data Setting the curve is simple Figure 6 Once all settings are defined click on Draw The graph is now finished Figure 7 Choose and parameter the distribution Al Normal law Binomial law C Gamma law Poisson law C Exponential law Negative binomial law C law Geometric law C Fisher Snedecor law Hypergeometric law Al C Student law C Mann Whitney distribution Wilcoxon sign rank test distribution Al N u o Mean u 15 8 Standard deviation o 2 2 Line type large dashed v 2 Width EL cuo M Draw Close Figure 6 Add a theoretical distribution curve to the graph 4 5 Saving graph s Once all graphs are drawn they can be saved by clicking on the save button of the navigation bar In the dialog box opening on the right of the interface select the device containing the graph to be saved the window number corresponds to the number automatically allocated by R under the guise R Graphics Device number Then choose the extension of the file to be created
7. new file must then be saved as Language_XX csv If you want to implement GrapheR in your language you are most welcome In that case remember that it would be a good idea but a tougher job to also translate the user manual The pdf version of this manual is contained in the doc directory of the package while the TFX version is contained in the vignettes directory Note that even if you are not TpX familiar the BTEX format file can be red and translated with script editors such as Tinn R or Notepad If you want to participate do not hesitate to contact me I will take care of all screenshots to be included in the manual and then add the link to the new language file in the code 10
8. raph Here the aim is to draw a histogram displaying the distribution of the size of African swallows We start by clicking on the Histogram button In the general parameters we choose Size as the variable to be represented and add that we want to retain only the values corresponding to the African level of the Species factor Figure 4 The histogram type is set to densities because as the warning says only this type allows to draw the distribution curve of the data All other settings are let to their default values except the title of the graph and those corresponding to the distribution curve we tick Draw the curve and define a color and a line type Once all necessary parameters are set the graph is drawn by clicking on the DRAW button of the navigation bar At this time you can choose to save the code producing your graph in an external R file If you answer Yes code of all graphs drawn in the same session will be added into this file If a new graphics device have to be beforehand opened click first on the window button see next section 4 3 Opening a new graphics device It is possible to draw graphs in different windows and or to draw several graphs in the same one To do this click on the window button of the navigation bar The dialog box that opens on the right of the interface allows specification of the window Dataset loaded Loading the dataset z Decimal separator poi Code for missing values Variab
9. several graphs can be drawn 4 draw a graph 5 adding elements to the graph From left to right add a horizontal line add a vertical line add any other kind of line add a theoretical distribution curve add text and add p values 6 saving graph s 7 diverse options user language and help 3 3 Messages frame When the mouse is over some specific elements of the GUI or when some specific actions are performed messages are displayed in this frame Three kinds of message can be displayed e in blue informative messages e in green warnings for when a particular attention should be payed to a specific point for example if this option is chosen then this one can not be e in red error messages for when the action requested can not be com pleted The message indicates the origin of the error 3 4 Settings block This block is divided into for to six sub blocks each containing options relating to a given theme general parameters of the graph title of the graph legend Each sub block can be opened or closed with the corresponding arrow situated on the right of the interface Of course defined settings are not lost when a sub block is closed 4 Use The example used here is based on the dataset provided in the package called Swallows To load it use the command data Swallows This fictional dataset exemplifies the legendary puzzle of African and European swallows migrations 4 1 Loading and modifying th

Introduction to GrapheR

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