CHANGES IN VERSION 1.12 ------------------------ - added max.overlaps and min.segment.length to provide further control over connectors. max.overlaps replaces maxoverlapsConnectors, but both can still be used for legacy purposes CHANGES IN VERSION 1.10 ------------------------ - added functionality to parse expressions in labels via parseLabels (TRUE/FALSE) - over-rides ggrepel's new default value for max.overlaps via introduction of maxoverlapsConnectors = 15 - user can now specify a direction for connectors via directionConnectors - removed labhjust and labvjust - added pCutoffCol (via Andrea Grioni) CHANGES IN VERSION 1.8 ------------------------ - added functionality to encircle variables of interest - added option to remove arrowheads on connectors - added option to rasterise images via ggrastr::geom_point_rast (Benjamin Ostendorf) - changed axis.text.y = element_text(..., vjust = 1.0) to 0.5 (Benjamin Ostendorf) CHANGES IN VERSION 1.6 ------------------------ - removed legendVisible and pLabellingCutoff parameters - deprecated transcriptPointSize, transcriptLabSize, transcriptLabCol, transcriptLabFace, transcriptLabhjust, transcriptLabvjust, boxedlabels, and drawconnectors parameters - now pad xlim by +/- 1 - moved default position of labels to be central to its respective point - added 'colGradient', which colours points continuously based on p-value CHANGES IN VERSION 1.4 ------------------------ - modified behaviour where a p-value of 0 is found: now converts these to 10^-1 * lowest non-zero p-value - added new paremeter 'legendLabels', which allows user to use expressions in the legend label - added support for tibbles - transcriptPointSize, transcriptLabSize, transcriptLabCol, transcriptLabFace, transcriptLabhjust, and transcriptLabvjust now deprecated. Use pointSize, labSize, labCol, labFace, labhjust, and labvjust, respectively, instead - pointSize default changed to 2.0 - boxedlabels now deprecated. Use boxedLabels CHANGES IN VERSION 1.2 ------------------------ - added functionality to shade specific genes in the plot space (parameters: shade, shadeLabel, shadeAlpha, shadeFill, shadeSize, shadeBins) - added new parameters 'labhjust' and 'labvjust' for fine tuning position of labels - suppress warnings about removal of missing values - now easier to hide the legend via legendVisible = TRUE/FALSE - changed 'colOverride' to 'colCustom' - added a new 'shape' parameter to control the shape of plotted points - added a new 'shapeCustom' parameter, akin to functionality supplied by 'colCustom' (formerly 'colOverride') - added functionality to add title, subtitle, and caption (parameters: title, subtitle, caption, titleLabSize, subtitleLabSize, captionLabSize = 12) - added functionality to add extra vertical and horizontal lines (parameters: hline, hlineType, hlineCol, hlineWidth, vline, vlineType, vlineCol, vlineWidth) - changed 'colConnectors' default from "black" to "grey10" - added extra parameters for line connectors (parameters: typeConnectors, endsConnectors, lengthConnectors) - 'labhjust' and 'labvjust' are now 'transcriptLabhjust' and 'transcriptLabvjust', respectively - user can now specify to draw transcript labels as text and text in boxes via 'boxedlabels' (TRUE/FALSE) - drawconnectors now deprecated. Use drawConnectors CHANGES IN VERSION 1.0.0 ------------------------ - user can now supply her/his/its own colour vector to label the points - default is to now draw grid lines and only have left and bottom borders - when selectLab is not NULL, even variables that do not pass the thresholds are now labelled along with those that do, even when DrawConnectors is either TRUE or FALSE. - correctly catches non-numeric x and / or y variables, and throws error. - the function now tolerates P values of 0 (zero) and replaces these with the lowest possible double value, given a user's specific computer architecture and R version.