杂记：seqkit计算fasta序列的长度和gc含量；ggpai

计算gc含量

seqkit.exe fx2tab --name --only-id --gc output.fasta -o gc.txt

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计算序列长度

seqkit.exe fx2tab --name --only-id -l output.fasta -o seqlen.txt

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ggpairs更改配色

这个只是一种方案，还有好多问题没有解决，比如如何给下三角和上三角赋予不同的颜色

代码

library(GGally)
ggpairs(iris,columns = 1:4,
        lower = list(continuous="points",
                     mapping=aes(color=Species)),
        diag = list(continuous="densityDiag",
                    mapping=aes(fill=Species)),
        upper = list(continuous="cor",
                     mapping=aes(colour=Species)))+
  scale_color_manual(values=c("red","blue","green"))+
  scale_fill_manual(values = c("orange","yellow","purple"))+
  theme_bw()

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ggplot2 作图 极坐标情况下添加直线

自己没有想法如何实现，搜索引擎搜索关键词 ggplot2 polar and then add straight lines
找到参考链接

https://stackoverflow.com/questions/66196451/draw-straight-line-between-any-two-point-when-using-coord-polar-in-ggplot2-r

代码暂时还看不明白，他是自己重新定义了一个函数，代码我先复制过来，后面有时间来研究

library(tidyverse)
library(ggplot2)
df <- tibble(x = rep(letters,  each = 5),
             y = rep(1:5, 26),
             d =  rnorm(26 * 5))


p1 <- ggplot() +
  geom_tile(data = df,
            aes(x = x,
                y = y,
                fill = d)) +
  ylim(c(-2, 5)) +
  geom_segment(
    aes(
      x = "o",
      y = -1,
      xend = "z",
      yend = 3
    ),
    arrow = arrow(length = unit(0.2, "cm")),
    col = "red",
    size = 2
  ) 
p1

image.png

p1 + coord_polar()

image.png

自定义函数

geom_segment_straight <- function(...) {
  layer <- geom_segment(...)
  new_layer <- ggproto(NULL, layer)
  old_geom <- new_layer$geom
  geom <- ggproto(
    NULL, old_geom,
    draw_panel = function(data, panel_params, coord, 
                          arrow = NULL, arrow.fill = NULL,
                          lineend = "butt", linejoin = "round",
                          na.rm = FALSE) {
      data <- ggplot2:::remove_missing(
        data, na.rm = na.rm, c("x", "y", "xend", "yend", 
                               "linetype", "size", "shape")
      )
      if (ggplot2:::empty(data)) {
        return(zeroGrob())
      }
      coords <- coord$transform(data, panel_params)
      # xend and yend need to be transformed separately, as coord doesn't understand
      ends <- transform(data, x = xend, y = yend)
      ends <- coord$transform(ends, panel_params)
      
      arrow.fill <- if (!is.null(arrow.fill)) arrow.fill else coords$colour
      return(grid::segmentsGrob(
        coords$x, coords$y, ends$x, ends$y,
        default.units = "native", gp = grid::gpar(
          col = alpha(coords$colour, coords$alpha),
          fill = alpha(arrow.fill, coords$alpha),
          lwd = coords$size * .pt,
          lty = coords$linetype,
          lineend = lineend,
          linejoin = linejoin
        ),
        arrow = arrow
      ))
      
    }
  )
  new_layer$geom <- geom
  return(new_layer)
}

画图代码

ggplot() +
  geom_tile(data = df,
            aes(x = x,
                y = y,
                fill = d)) +
  ylim(c(-2, 5)) +
  geom_segment_straight(
    aes(
      x = "o",
      y = -1,
      xend = "z",
      yend = 3
    ),
    arrow = arrow(length = unit(0.2, "cm")),
    col = "red",
    size = 2
  ) + 
  coord_polar()

image.png

曲线也是可以的

geom_curve_polar <- function(...) {
  layer <- geom_curve(...)
  new_layer <- ggproto(NULL, layer)
  old_geom <- new_layer$geom
  geom <- ggproto(
    NULL, old_geom,
    draw_panel = function(data, panel_params, coord, 
                          curvature = 0.5, angle = 90, ncp = 5,
                          arrow = NULL, arrow.fill = NULL,
                          lineend = "butt", linejoin = "round",
                          na.rm = FALSE) {
      data <- ggplot2:::remove_missing(
        data, na.rm = na.rm, c("x", "y", "xend", "yend", 
                               "linetype", "size", "shape")
      )
      if (ggplot2:::empty(data)) {
        return(zeroGrob())
      }
      coords <- coord$transform(data, panel_params)
      ends <- transform(data, x = xend, y = yend)
      ends <- coord$transform(ends, panel_params)
      
      arrow.fill <- if (!is.null(arrow.fill)) arrow.fill else coords$colour
      return(grid::curveGrob(
        coords$x, coords$y, ends$x, ends$y,
        default.units = "native", gp = grid::gpar(
          col = alpha(coords$colour, coords$alpha),
          fill = alpha(arrow.fill, coords$alpha),
          lwd = coords$size * .pt,
          lty = coords$linetype,
          lineend = lineend,
          linejoin = linejoin
        ),
        curvature = curvature, angle = angle, ncp = ncp,
        square = FALSE, squareShape = 1, inflect = FALSE, open = TRUE,
        arrow = arrow
      ))
      
    }
  )
  new_layer$geom <- geom
  return(new_layer)
}

ggplot() +
  geom_tile(data = df,
            aes(x = x,
                y = y,
                fill = d)) +
  ylim(c(-2, 5)) +
  geom_curve_polar(
    aes(
      x = "o",
      y = -1,
      xend = "z",
      yend = 3
    ),
    arrow = arrow(length = unit(0.2, "cm")),
    col = "red",
    size = 2
  ) + 
  coord_polar()

image.png