Question

我正在尝试制作一个ggplot散点图，该图会根据提供给函数feature的{{1}}选项添加三层之一：

tsnePlotSubcluster

如果为feature = c("subcluster" , "area" , "age")，则添加的图层应标出属于指定子集群的点（单元）。

如果为feature == "subcluster"，则添加的图层应绘制属于指定子群集的相同图层，但这次由其区域着色。

如果为feature == "area"，则添加的图层应绘制属于指定子群集的相同图层，但这次由其区域着色。

我可以在3个不同的函数中执行此操作，但是当我尝试使用feature == "age"语句将它们添加到单个函数中时，出现以下错误：

if

tsne.clust <- tsnePlotSubcluster(subclust = "cluster_2", feature = "area") Error: Cannot add ggproto objects together. Did you forget to add this object to a ggplot object?看起来像这样：（下面是reprex）

df

我尝试合并所有三个选项进行绘制的函数是：

                   cell.name      tSNE_1      tSNE_2 nGene Age          area subcluster.merge
18513 TCAGCAATCCCTCAGT_235875  17.1932545  20.9951805   994  25      parietal       cluster_23
45195  CACATTTAGTGTACCT_55869   2.0990437  -3.1644088   605  14         motor       cluster_16
437    ACTGCTCAGCTGGAAC_60204  14.3391798   5.7986418   919  17     occipital    cluster_12-35
47652  TTGAACGAGCGGCTTC_24246  -2.4054652  -5.7217611   617  17         motor       cluster_16
3079   CTGAAGTGTCCGAGTC_36162  13.3077568  -9.8810075  2360  19      parietal    cluster_10-34
73692  TACGGTATCCACGTTC_43045  -3.9540697 -22.1901588   757  25        insula cluster_19-20-40
78111  ACGGGTCAGGAGTTGC_52675  -8.2138674  -5.6368533   680  14         motor       cluster_11
77792  TTGAACGGTCTAGAGG_46399  -4.8505234 -17.3649528  1495  25        insula cluster_19-20-40
80576  ACGAGGACACCCAGTG_43377   4.7608973  12.3166870   652  17           PFC       cluster_27
40102 CTAGCCTTCGGATGTT_108090 -26.0839271  -6.0513843  2877  18     occipital       cluster_17
75778 GAATGAATCGAACGGA_122697  -0.8466168 -21.6881664   681  25           PFC cluster_19-20-40
64808 CTGGTCTCAGTCCTTC_220448   1.4123929  23.1787489  1275  25      parietal       cluster_21
31050 CGATGGCGTCGCCATG_107147  12.7008032 -23.3682646  1457  25      temporal     cluster_5-24
40011 AAGGCAGCAAGCCCAC_103547 -15.8308776  -9.0420539  2830  18     occipital       cluster_15
23802 TTAGGCACATCGGTTA_224119  25.8490750   5.6472168  2354  25      parietal     cluster_7-39
55771  CGGAGTCGTGACGCCT_22310  -0.1658289   9.2474600   920  22         motor       cluster_13
62142 TAGAGCTAGGTGACCA_270328  -1.8325109 -12.8780762  2493  25     cingulate        cluster_4
85340 AGGTCATCAAGCGATG_108496 -18.5638069  19.3544782  1054  20         motor       cluster_21
31185 TGGCCAGGTGCTGTAT_271635   5.3272499 -19.8372034  1557  25     cingulate       cluster_29
496    AGAGTGGGTTGTGGCC_10259  11.5646170  11.4089743  1549  18   hippocampus        cluster_8
2513   GATCTAGTCCAAGCCG_14125   7.6368712  11.6917014  1756  19         motor        cluster_8
52795  TACACGATCAGTCCCT_43422  -0.8565756  12.8355195  1534  20           PFC       cluster_13
44355  TCTATTGGTCACAAGG_44401 -21.1689622  -8.1854890  1382  25        insula        cluster_1
96327 GATCTAGTCGCTTAGA_232432 -26.6976718  10.3691109   877  25      parietal     cluster_3-33
41100  GTTACAGGTATGAAAC_43797 -21.6719857   0.6879885  1489  19 somatosensory     cluster_3-33

reprex：

tsnePlotSubcluster <- function(feature = "subcluster", # can be area, age, subcluster
                               subclust = "cluster_1",
                               size.grey = 0.25, 
                               size.color = 0.3
                               ) {

  # params <- plot.params[[celltype]]
  # cluster.colors <- color.values[[celltype]]$i

   p <- ggplot(tsne.meta) + 

     # Plot cells in all other subclusters in grey.
       geom_point(data = filter(tsne.meta, ! subcluster.merge == subclust),
                  aes(tSNE_1, tSNE_2, alpha = nGene), 
                  colour = "grey90", size = size.grey) +

        # a) Highlight subcluster:
        # Plot cells from selected subcluster in color.
        {if(feature == "subclust")
            geom_point(data = filter(tsne.meta, subcluster.merge == subclust), 
                  aes(tSNE_1, tSNE_2, color = nGene, alpha = nGene),
                  size = size.color) + 
            theme(legend.position = 'none') +
            scale_color_viridis_c(option = "plasma", begin = 0.1, end = 0.6)} +

        #  b) Color subcluster cells by age:
         {if(feature == "age")
             geom_point(data = filter(tsne.meta, subcluster.merge == subclust), 
                      aes(tSNE_1, tSNE_2, color = Age, alpha = nGene),
                      size = size.color) + 
             scale_color_viridis_d(option = "plasma") +
             theme(legend.position = 'top')} +

         #  c) Color subcluster cells by area:
         {if(feature == "area")
             geom_point(data = filter(tsne.meta, subcluster.merge == subclust), 
                      aes(tSNE_1, tSNE_2, color = area, alpha = nGene),
                      size = size.color) + 
             scale_color_viridis_d(option = "viridis") +
             theme(legend.position = 'top')} +

  labs(title = paste(celltype, "|", subclust)) +

  theme(plot.subtitle = element_text(color="grey18", size=11, family="Helvetica", face = "plain", hjust = 0.5),
        plot.title = element_text(color="grey18", size=12, family="Helvetica", face = "plain"),
        axis.title = element_blank(),
        axis.text = element_blank(),
        axis.ticks = element_blank(),
        axis.line = element_blank(),
        panel.background = element_blank(),
        panel.grid = element_blank()
    )

   return(p)
   # png(paste0("tSNE_", celltype, "_", subclust,".png"), height = 5, width = 6, units = 'in', res = 300)
   # print(p)
   # dev.off()
}

Answer 1

请尝试将层附加到ggplot对象，而不要使用一个大表达式。这样，您可以添加一些有关添加哪些图层的逻辑。请注意，没有tsne.meta，我无法真正进行测试。

tsnePlotSubcluster <- function(feature = "subcluster", # can be area, age, subcluster
                               subclust = "cluster_1",
                               size.grey = 0.25, 
                               size.color = 0.3) {

  # params <- plot.params[[celltype]]
  # cluster.colors <- color.values[[celltype]]$i

  p <- ggplot(tsne.meta) + 

    # Plot cells in all other subclusters in grey.
    geom_point(data = filter(tsne.meta, ! subcluster.merge == subclust),
               aes(tSNE_1, tSNE_2, alpha = nGene), 
               colour = "grey90", size = size.grey)

  # a) Highlight subcluster:
  # Plot cells from selected subcluster in color.
  if(feature == "subclust") {
    p <- p + geom_point(data = filter(tsne.meta, subcluster.merge == subclust), 
                        aes(tSNE_1, tSNE_2, color = nGene, alpha = nGene),
                        size = size.color) + 
      theme(legend.position = 'none') +
      scale_color_viridis_c(option = "plasma", begin = 0.1, end = 0.6)
  }
  #  b) Color subcluster cells by age:
  else if(feature == "age") {
    p <- p + geom_point(data = filter(tsne.meta, subcluster.merge == subclust), 
                        aes(tSNE_1, tSNE_2, color = Age, alpha = nGene),
                        size = size.color) + 
      scale_color_viridis_d(option = "plasma") +
      theme(legend.position = 'top')
  }

  #  c) Color subcluster cells by area:
  else if(feature == "area") {
    p <- p + geom_point(data = filter(tsne.meta, subcluster.merge == subclust), 
                        aes(tSNE_1, tSNE_2, color = area, alpha = nGene),
                        size = size.color) + 
      scale_color_viridis_d(option = "viridis") +
      theme(legend.position = 'top')
  }

  p <- p + labs(title = paste(celltype, "|", subclust)) +

    theme(plot.subtitle = element_text(color="grey18", size=11, family="Helvetica", face = "plain", hjust = 0.5),
          plot.title = element_text(color="grey18", size=12, family="Helvetica", face = "plain"),
          axis.title = element_blank(),
          axis.text = element_blank(),
          axis.ticks = element_blank(),
          axis.line = element_blank(),
          panel.background = element_blank(),
          panel.grid = element_blank()
    )

  return(p)
  # png(paste0("tSNE_", celltype, "_", subclust,".png"), height = 5, width = 6, units = 'in', res = 300)
  # print(p)
  # dev.off()
}

您可能还想看看programmatic aes

根据函数变量的值有条件地将层添加到gglplot中

1 个答案: