R/plot.R

In OliverXUZY/waveST: Wavelet-Based Spatial Transcriptomic Dimensionality Reduction

## The plot function
theme_set(theme_minimal())

#' plot function for waveST class
#'
#' visualize the top factor genes and top 5 genes with high loadings on certain factor genes
#' @docType methods
#' @export
#' @param x An object of class \code{\link{waveST}}.
#' @param k which factor gene to visualize
#' @param wave whether use wavelet method
#' @param ... Plot parameters forwarded.
#' @return A plot object.
methods::setMethod(
  "plot",
  c(x = "waveST", y = "missing"),
  function(x, k = 1, wave = TRUE, ...) {
    waveST = x
    lay = layout(matrix(1:6, 2, 3, byrow = TRUE))
    ######## ============== show on raw
    if (!wave) {
      waveST@output$f[, k] %>%
        # normalize1() %>%
        matrix(nrow = sqrt(length(.))) %>%
        image(., asp = 1, xaxt = "n", yaxt = "n")


      ids = waveST@output$l[, k] %>%
        abs() %>%
        order(decreasing = T)

      waveST@input[, ids[1:5]] %>%
        map(~ matrix(.x, nrow = sqrt(length(.x)))) %>%
        map(~ image(.x, asp = 1, xaxt = "n", yaxt = "n"))
    } else if (wave) {
      waveST@output$f[, k] %>%
        InvWaveTrans(., waveST@input %>% as.matrix()) %>%
        image(., asp = 1, xaxt = "n", yaxt = "n")


      ids = waveST@output$l[, k] %>%
        abs() %>%
        order(decreasing = T)

      for (j in seq_len(5)) {
        if (!is.matrix(waveST@input)) {
          waveST@input = as.matrix(waveST@input)
        }

        waveST@input[, j] %>%
          WaveTransCoefs(wf = "d4", J = 5, thresholdMethod = "manual", tau = 40) %>%
          unlist() %>%
          InvWaveTrans(raws = waveST@input %>% as.matrix()) %>%
          matrix(., nrow = sqrt(length(.))) %>%
          image(., asp = 1, xaxt = "n", yaxt = "n")
      }
    }
    layout(1)
  }
)