如何将pheatmap绘图绘制到屏幕并保存到文件-Howtodrawpheatmapplottoscreenandalsosavetofile

2  

The authors of pheatmap didn't seem to make this super easy. But it's something you are going to need to do in two separate steps. First, we use the sample data from the ?pheatmap help page

pheatmap的作者似乎并没有让这非常容易。但这是你需要分两步完成的事情。首先，我们使用来自？pheatmap帮助页面的示例数据

test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")

We can render the plot and save the result with

我们可以渲染绘图并保存结果

xx <- pheatmap(test)

Then you can output to this to a file by opening a graphics device and re-drawing the result the way it's done in the main function

然后你可以通过打开一个图形设备输出到这个文件，然后按照在main函数中完成的方式重新绘制结果

save_pheatmap_pdf <- function(x, filename, width=7, height=7) {
   stopifnot(!missing(x))
   stopifnot(!missing(filename))
   pdf(filename, width=width, height=height)
   grid::grid.newpage()
   grid::grid.draw(x$gtable)
   dev.off()
}
save_pheatmap_pdf(xx, "test.pdf")

This package uses the grid library directly and does not use ggplot2 so solutions for that package would be different. The ggsave function makes it easier to save the last drawn plot to a file.

该软件包直接使用网格库，不使用ggplot2，因此该软件包的解决方案会有所不同。 ggsave函数可以更容易地将最后绘制的绘图保存到文件中。

0  

FYI, I made a more complex function that includes making the pheatmap and then calling the save_heatmap function from above. I'm posting it here if it is useful to anyone, and also for critiques. I added in a line to save the heatmap image file with the name of the matrix that gives rise to the heatmap. This is helpful for downstream organization of the files.

仅供参考，我做了一个更复杂的功能，包括制作pheatmap，然后从上面调用save_heatmap函数。如果它对任何人都有用，我也会在这里发布，也可以用于批评。我添加了一行来保存热图图像文件，其中包含产生热图的矩阵名称。这有助于下游组织文件。

save_pheatmap <- function(x, filename, width=480, height=960) {
   stopifnot(!missing(x))
   stopifnot(!missing(filename))
   png(filename,width = width, height=height)
   grid::grid.newpage()
   grid::grid.draw(x$gtable)
   dev.off()
}

plot_heatmap <- function(mat,color=NULL, cluster_rows=NULL, cluster_cols=NULL, scale=NULL, 
  cellwidth=NULL, cellheight=NULL,show_colnames=NULL, labels_col=NULL, show_rownames=NULL,
  border_color=NULL,legend=NULL,...){

  #Default Color
  if (is.null(color)){
    color=rev(col.pal)
  }

  #Default cluster
  if (is.null(cluster_rows)){
    cluster_rows=FALSE
  }

  if (is.null(cluster_cols)){
    cluster_cols=FALSE
  }

  #Default sclae
  if(is.null(scale)){
    scale="none"
  }

  #Default cell dims
  if (is.null(cellwidth)){
    cellwidth=12
  }

  if (is.null(cellheight)){
    cellheight=12
  }

  #Default Labels

  if (is.null(show_colnames)){
    show_colnames=TRUE
  }

  if (is.null(labels_col)){
    labels_col=NULL
  }

  if (is.null(show_rownames)){
    show_rownames=FALSE
  }

  #Set border

  if (is.null(border_color)){
    border_color=NA
  }

  #Legend

  if (is.null(legend)){
    legend=FALSE
  }


  temp_hm <- pheatmap(mat,color=color, cluster_rows=cluster_rows, cluster_cols=cluster_cols, scale=scale, 
  cellwidth=cellwidth, cellheight=cellheight,show_colnames=show_colnames, labels_col=labels_col,
  show_rownames=show_rownames,border_color=border_color,legend=legend)

  temp_hm_name <- paste(deparse(substitute(mat)),".png", sep="")

  save_pheatmap(temp_hm, filename=temp_hm_name)

}

}

0  

The wplot_save_this() function in the MarkdownReports saves any displayed plot to a .pdf file. Also, all other plotting functions in the package (wbarplot (), whist(), wplot(), etc ) display and save respective as .pdf automatically as well as linking them to a Markdown notebook/ report.

MarkdownReports中的wplot_save_this（）函数将任何显示的绘图保存为.pdf文件。此外，包中的所有其他绘图功能（wbarplot（），whist（），wplot（）等）会自动显示和保存为.pdf，并将它们链接到Markdown笔记本/报告。