diff --git a/R/visualization.R b/R/visualization.R index dac247e..27f53b0 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -560,9 +560,9 @@ transparentCol <- function(color, percent = 50, name = NULL) { #' @param pSigThresh numeric; the two-sided P value significance threshold. It #' can be used in place of the zSigThresh parameter. If no value is provided, #' the zSigThresh will be used. -#' @param zscoreLimit numeric; limit the Z-score to look better in the graph -#' scale gradient. Z-score values above zscoreLimit will be represented as -#' zscoreLimit, scores below -zscoreLimit will be represented as -zscoreLimit +#' @param zScoreLimit numeric; limit the Z-score to look better in the graph +#' scale gradient. Z-score values above zScoreLimit will be represented as +#' zScoreLimit, scores below -zScoreLimit will be represented as -zScoreLimit #' (default: NULL). #' @param reorder boolean; if TRUE, reorder the cell types by clustering on the #' z-score. If false, orders in alphabetical order (default: FALSE). @@ -587,7 +587,7 @@ transparentCol <- function(color, percent = 50, name = NULL) { #' #' @export vizColocDotplot <- function(dat, zSigThresh = 1.96, pSigThresh = NULL, - zscoreLimit = NULL, reorder = FALSE, + zScoreLimit = NULL, reorder = FALSE, symmetrical = FALSE, onlySignificant = FALSE, colors = c("blue", "white", "red"), dotSizes = c(6,31)){ @@ -612,9 +612,9 @@ vizColocDotplot <- function(dat, zSigThresh = 1.96, pSigThresh = NULL, dplyr::filter(scale == min(scale, na.rm = TRUE)) ## limit the z-score for the gradient in the figure to look better - if (!is.null(zscoreLimit)) { - sig_dat$Z[sig_dat$Z > zscoreLimit] <- zscoreLimit - sig_dat$Z[sig_dat$Z < -zscoreLimit] <- -zscoreLimit + if (!is.null(zScoreLimit)) { + sig_dat$Z[sig_dat$Z > zScoreLimit] <- zScoreLimit + sig_dat$Z[sig_dat$Z < -zScoreLimit] <- -zScoreLimit } ## scale sizes