Installation

rmarkdown
tinytex
pandoc
预先要安装好以上几个包。

R Markdown生成PowerPoint原理

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使用示例

讲解视频 https://www.youtube.com/watch?v=uiA3znJb4KM
具体参数和步骤： https://support.rstudio.com/hc/en-us/articles/360004672913-Rendering-PowerPoint-Presentations-with-the-RStudio-IDE
Rmarkdown生成PPT：https://bookdown.org/yihui/rmarkdown/powerpoint-presentation.html
github示例：https://github.com/sol-eng/powerpoint

传参

1、通过params设置

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2、通过R code读入

注意：R code要设置不打印出来，不然code会显示在ppt上面。

config=yaml.load_file("config.yml")
species = config$species ##human or mouse
sample <- config$sample
rawname <- config$rawname
cellrangerdir <- config$dataDir
outdir <- config$analysisDir

字体设置

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插入图片

1、已知图片名、路径，直接插入

![image description](imageName.png){50%width}

## fig.align设置fig位置，fig.cap设置fig的说明
knitr::include_graphics('images/hex-rmarkdown.png')

2、文件路径或名称不明确，带入变量插入

如果需要对文件名进行匹配显示，或者代码匹配未知个同样文件名规律的图片，放置在PPT中，可以使用cat进行打印操作，示例如下：
（1）文件路径为变量，使用cat和paste0结合

cat(paste0("[图片上传失败...(image-a760c0-1634006991616)]")))

（2）根据文件数量生成对应个数的幻灯片页面，和与内容对应的标题

# 1、根据文件名规律获取文件列表
img_list <- list.files( path = 'images',  pattern = '*.png$', full.names=T, recursive=FALSE)
img_list <- img_list[grep("top8",img_list)]
# 2、依次生成幻灯片，每张放置两张图片，注意每页的标题，以及换行
for (n in 1:length(img_list)){
  img1 <- paste0("index_files/figure-html/top8Markers.DimPlot-",n,".png")
  img2 <- paste0("index_files/figure-html/top8Markers.DimPlot-",n+1,".png")
  if (file.exists(img2)){
    cat(paste0("## Cluster-specific genes", " (Top 8, Cluster ",n-1,",",n,")", "\n\n" ,
      ":::::::::::::: {.columns}", "\n", "::: {.column}","\n\n",
      "[图片上传失败...(image-a2ae3a-1634006991616)]\n\n",
      ":::\n","::: {.column}","\n\n",
      "[图片上传失败...(image-aa7455-1634006991616)]\n\n",
      ":::\n","::::::::::::::\n")
      )
  }else{
    cat(paste0("## Cluster-specific genes", " (Top 8, Cluster ",n,")", "\n\n" ,
      "[图片上传失败...(image-decf88-1634006991616)]
      )
  }
  n <- n+2
}
cat("  \n")

打印出来是这样的：

## Cluster-specific genes (Top 8, Cluster 0,1)

:::::::::::::: {.columns}
::: {.column}

![](index_files/figure-html/top8Markers.DimPlot-1.jpeg)

:::
::: {.column}

![](index_files/figure-html/top8Markers.DimPlot-2.jpeg)

:::
::::::::::::::
## Cluster-specific genes (Top 8, Cluster 2,3)

:::::::::::::: {.columns}
::: {.column}

![](index_files/figure-html/top8Markers.DimPlot-3.jpeg)

:::
::: {.column}

![](index_files/figure-html/top8Markers.DimPlot-4.jpeg)

:::
::::::::::::::

插入表格

写法跟markdown一样，这里不再赘述。

 manufacturer    displ   hwy     class
-------------    ------  -----  ---------
        audi     1.8     29      compact
   chevrolet     5.3     20        suv
       dodge     2.4     24      minivan

Table: Simple table syntax and caption.

表的注释方法为 Table: 注释内容，PPT中文字会出现在表的下方。例如：

Table: Gene expression visualization of widely occurring cell type markers. The following cell type markers are plotted.

|  Gene   | Common cell type   |
|:-: | :-:
| EPCAM | Epithelial |
| CD3D | T cell |
| CD14 | Monocyte |
| CD68 | Macrophage |
| B cells | CD19 |
| PECAM1 | Endothelial |
| COL1A2 | Fibroblast |
| NCAM1 | NK |
| MZBI |Plasma |
| TPSAB1 | Mast |

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插入dataframe

knitr::kable(stat,align = 'c', format = "markdown")

分列

这个功能在ppt排版时非常常用

:::::::::::::: {.columns}
::: {.column}
contents...
:::
::: {.column}
contents...
:::
::::::::::::::

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演讲者笔记

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使用ppt模板

在Rmarkdown文件开头yml中设置output格式为powerpoint_presentation，reference_doc给到你想使用的模板文件。

---
title: "Visium Standard Analysis Report"
date: "`r Sys.Date()`"
output: 
  powerpoint_presentation:
    df_print: kable
    slide_level: 2
    reference_doc: template.pptx
---

生成PPT

R代码

rmarkdown::render("in.Rmd", output_format = "powerpoint_presentation")

Rstudio

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