Don‘t know how to automatically pick scale for object of type ＜tbl_df/tbl/data.frame＞. Defaulting t

> data_long
# A tibble: 1,459,188 × 6
     AM1 group  clusters          `Tissue structure` CellType                                                 Value
   <dbl> <chr>  <chr>             <chr>              <chr>                                                    <dbl>
 1 0.352 SiO2_7 Interstitial zone Alveolar           NAKAMURA_BRONCHIAL_AND_BRONCHIOLAR_EPITHELIA          349.    
 2 0.352 SiO2_7 Interstitial zone Alveolar           GOBP_ESTABLISHMENT_OF_LEFT_RIGHT_ASYMMETRY             -0.158 
 3 0.352 SiO2_7 Interstitial zone Alveolar           GOBP_AXONEMAL_CENTRAL_APPARATUS_ASSEMBLY                0.0180
 4 0.352 SiO2_7 Interstitial zone Alveolar           HP_ABNORMAL_RESPIRATORY_MOTILE_CILIUM_PHYSIOLOGY        0.0167
 5 0.352 SiO2_7 Interstitial zone Alveolar           HP_COILED_SPERM_FLAGELLA                               -0.115 
 6 0.352 SiO2_7 Interstitial zone Alveolar           GOBP_INNER_DYNEIN_ARM_ASSEMBLY                         -0.108 
 7 0.352 SiO2_7 Interstitial zone Alveolar           HP_ABNORMAL_SPERM_TAIL_MORPHOLOGY                      -0.110 
 8 0.352 SiO2_7 Interstitial zone Alveolar           GOBP_AXONEME_ASSEMBLY                                  -0.0562
 9 0.352 SiO2_7 Interstitial zone Alveolar           REACTOME_CONJUGATION_OF_BENZOATE_WITH_GLYCINE          -0.03  
10 0.352 SiO2_7 Interstitial zone Alveolar           GOBP_DETERMINATION_OF_PANCREATIC_LEFT_RIGHT_ASYMMETRY  -0.105 
# ℹ 1,459,178 more rows
# ℹ Use `print(n = ...)` to see more rows
>  ggplot(data_long, aes(x = data_long[, my_desired_celltype], y = data_long[,"Value"])) +
+     geom_point()
Don't know how to automatically pick scale for object of type <tbl_df/tbl/data.frame>. Defaulting to continuous.
Don't know how to automatically pick scale for object of type <tbl_df/tbl/data.frame>. Defaulting to continuous.
Error in `data[[var]][scale_index[[i]]]`:
! Can't subset columns past the end.
ℹ Locations 2, 3, 4, …, 1459187, and 1459188 don't exist.
ℹ There is only 1 column.
Run `rlang::last_trace()` to see where the error occurred.
Warning message:
In geom_point() :
  All aesthetics have length 1, but the data has 1459188 rows.
ℹ Did you mean to use `annotate()`?
>   

解释：

1. aes(x = !!sym(my_desired_celltype), y = Value)：这里的 !!sym(my_desired_celltype) 是为了动态地将 my_desired_celltype 变量作为列名传入，确保 ggplot 正确找到对应的列。
2. Value 列不需要加索引，可以直接使用它的名字。

如果 my_desired_celltype 是一个字符变量，指代列名（如 "CellType"），你可以使用 !!sym(my_desired_celltype) 来动态解析这个列名。如果列名是直接写入代码中的话，你可以直接这样写：

r

复制代码

# 如果列名已知，直接使用 ggplot(data_long, aes(x = CellType, y = Value)) + geom_point()

这样可以避免索引超出范围的错误。

Imagine you're setting up a scene for a play, with each actor in the right place. But when the curtain rises, suddenly, all the actors are in the wrong spots! This is a little like what happened with your code. Here's how the story unfolds:

You’ve got a huge cast of characters—over 1.4 million rows of data in your data_long tibble. And you're asking ggplot2 to set the stage by mapping values from two columns: my_desired_celltype and Value. But there's a mix-up: you're using data_long[, my_desired_celltype] to grab one of your actors, which refers to an entire data frame instead of a single column. That’s why ggplot2 doesn't know how to handle this—it’s like handing it a whole crew instead of just one actor.

Here's the fix: instead of indexing the data within ggplot, let’s tell the plot exactly which columns to use in a more direct way. We'll point ggplot to the right column names, like this:

r

复制代码

ggplot(data_long, aes(x = !!sym(my_desired_celltype), y = Value)) + geom_point()

In this version of the story, the sym() function from the rlang package turns your my_desired_celltype string into a symbol that ggplot understands, ensuring that the correct column is selected for the x-axis. The !! operator then unquotes it, allowing ggplot to treat it like a column.

Now, when the curtain rises again, everything is in its right place: your data actors are set, and the show (your plot) can go on!

正确写法

  ggplot(data_long, aes(x = !!sym(my_desired_celltype), y = Value)) +
    geom_point() +
    geom_smooth(method = "lm") +
    facet_wrap(~ CellType) +  # This automatically uses the column names
    labs(x = paste0(my_desired_celltype), y = "", title = "Correlation with AT2_coarse") +
    theme_classic() +
    scale_fill_manual(values = c("blue", "green", "red")) +
    theme(
      axis.text.x = element_text(angle = 45, vjust = 0.5, hjust = 0.5),
      axis.text.y = element_text(size = 12),
      axis.text = element_text(color = 'black', size = 12),
      plot.title = element_text(family = '', face = 'bold', colour = 'black', size = 12,
                                hjust = 0.5, vjust = 0.5)  ## Title centered
    )