sjri's questions

我使用 R 中的 ggplot2 创建一个点图，其中 x 轴是变量名，y 轴是细胞系 ID。该图由组变量（“焦点形成”、“软琼脂”、“3D 基质胶生长”）构成。

我想要水平旋转或翻转整个图，以便：

目前在左边的变成了右边的（反之亦然）。

方面标签（当前位于左侧）移动到右侧。

ID 标签（当前位于右侧）移至左侧。

简而言之，我想要当前图在垂直轴上的镜像，就像沿 y 轴旋转 180 度一样。

这是我正在使用的代码和数据：

library(dplyr)
library(tidyverse)
library(ggplot2)

df1 <- structure(list(ID = c("OVCAR3", "OVCR", "AFC", "OVCAR3", "OVCR", "AFC", 
                             "OVCAR3", "OVCR", "AFC"), 
                     V = c(1.467, 1.402, 1.445, 1.48, 1.313, 1.418, 1.5, 1.456, 1.489), 
                     N = c(0.823, 0.762, 0.34, 0.738, 0.739, 0.533, 0.891, 0.904, 0.412), 
                     A = c(0.734, 0.771, 1.098, 0.793, 0.799, 0.938, 1.12, 0.853, 1.076), 
                     `N+A` = c(-1.075, -0.577, -0.832, -1.025, -0.633, -0.977, -1.21, -0.517, -1.032), 
                     C = c(-0.239, 0.342, 0.33, -0.314, 0.341, 0.202, -0.324, 0.303, 0.207), 
                     `N+C` = c(-1.403, -1.002, -1.162, -1.5, -1.106, -1.22, -1.329, -1.043, -1.164), 
                     T = c(0.113, 0.487, 0.393, -0.105, 0.336, 0.366, 0.089, 0.329, 0.275), 
                     `N+T` = c(-1.25, -1.045, -1.066, -1.206, -0.981, -0.928, -1.321, -1.12, -1.032), 
                     Group = c("Foci formation", "Foci formation", "Foci formation", 
                               "Soft agar", "Soft agar", "Soft agar", 
                               "3D Matrigel growth", "3D Matrigel growth", "3D Matrigel growth")),
                class = "data.frame", row.names = c(NA, -9L))

# Convert to long format
df_long <- df1 %>% 
  pivot_longer(cols = V:`N+T`, names_to = "Variable", values_to = "Z_score")

# Create dot plot
ggplot(df_long, aes(x = Variable, y = ID, color = Z_score, size = abs(Z_score))) +
  geom_point() +
  facet_grid(rows = vars(Group), scales = "free_y", space = "free_y") +
  scale_color_gradient2(low = "blue", mid = "white", high = "red", midpoint = 0) +
  theme_minimal() +
  theme(
    axis.text.x = element_text(angle = 45, hjust = 1),
    strip.text.y = element_text(angle = 0)
  ) +
  labs(x = "Variables", y = "Cell Line", color = "Z-Score", size = "Magnitude")

输出：

我正在尝试使用 GraphQL API 从 gnomAD 数据库获取变体详细信息，包括种群等位基因频率 ( af)。但是，查询不会返回种群的等位基因频率。当我af在 下添加时populations，出现以下错误：

GraphQLError: Cannot query field 'af' on type 'VariantPopulation'. Did you mean 'ac' or 'an'?

GraphQL request:10:9
 9 |         populations {
10 |         af
   |         ^
11 |         id

我的疑问：

from gql import gql, Client
from gql.transport.aiohttp import AIOHTTPTransport

# GraphQL query to fetch variant details
query = gql(
"""
query VariantsInGene {
    gene(gene_symbol: "PTH", reference_genome: GRCh38) {
        variants(dataset: gnomad_r4) {
            variant_id
            pos
            exome {
                af
                populations {
                    id
                    af
                }
            }
        }
    }
}
"""
)

res = await client.execute_async(query)

我尝试过的：

• 在外显子组水平获取等位基因频率（af） （工作正常）。
• 添加af内部populations（导致错误）。
• 检查可用字段VariantPopulation（建议ac和an，但不建议af）。

问题：

如何在 gnomAD GraphQL 中检索每个人群的等位基因频率 (af ) ？如果我从查询中删除 af，它会执行，但不会检索到人群的 af：

我正在尝试使用 R 中的 ggplot2 向散点图中的点添加文本标签。但是，添加文本标签后，与这些标签相关的点会错位。这是我的代码的简化版本：

library(ggplot2)
library(ggrepel)
library(dplyr)

df = data.frame(structure(list(FC = c(4.712, 4.8264, 0.078026, 0.098754, 11.612, 
0.21181, 6.1715, 0.15113, 0.19936, 0.23572, 0.23564, 6.9851, 
5.2465, 12.641, 4.4164, 0.24834, 7.4598, 5.1384, 0.18861, 0.24986
), log2FC = c(2.2363, 2.271, -3.6799, -3.34, 3.5375, -2.2391, 
2.6256, -2.7261, -2.3266, -2.0849, -2.0853, 2.8043, 2.3914, 3.6601, 
2.1429, -2.0096, 2.8991, 2.3613, -2.4065, -2.0008), Identifier = 1:20), row.names = c("3-Indoleacetic acid", 
"4-Hydroxyphenylpyruvic acid", "Adenine", "Adenosine", "alpha-Ketoglutaric acid", 
"C10", "C18:1OH", "Deoxyadenosine", "Deoxycytidine", "Deoxyguanosine", 
"Histamine", "Homocitrulline", "Indolelactic acid", "Kynurenine", 
"Leucine", "LysoPC a C20:4", "N-Acetylputrescine", "Phenylalanine", 
"Phenylethylamine", "Spermidine"), class = "data.frame"))


show.names = c("Kynurenine", "alpha-Ketoglutaric acid", "N-Acetylputrescine", "Homocitrulline", "C18:1OH", "Deoxycytidine", "Phenylethylamine", "Deoxyadenosine", "Adenosine", "Adenine")

p1 = ggplot(df, aes(x = Identifier, y = log2FC)) +
     geom_point(aes(color = log2FC >= 0)) +
     scale_color_manual(name = "Group", values = c("red", "blue"), labels = c("Down", "Up")) +
     geom_text_repel(data = df[rownames(df) %in% show.names,], aes(label = show.names)) +
     geom_hline(yintercept = 0, linetype = "solid") +
     labs(x = "Compounds", y = "Log2 Fold Change") + theme_minimal()
p1

在生成的图中，点与标签未正确对齐。例如，“Kynurenine”具有正值（3.6601），但它们显示在图中的负值（接近 -4）区域

有人能帮助我理解为什么当我添加文本标签时点会放错位置，以及如何解决这个问题？

我想按照特定的顺序安排情节。

library(ggpubr)
data("ToothGrowth")
data("mtcars")
mtcars$name <- rownames(mtcars)
mtcars$cyl <- as.factor(mtcars$cyl)

# create boxplot
bxp <- ggboxplot(ToothGrowth, x = "dose", y = "len", color = "dose", palette = "jco")
# create dotplot
dp <- ggdotplot(ToothGrowth, x = "dose", y = "len", color = "dose", palette = "jco", binwidth = 1)

# create scatterplot
sp = ggscatter(mtcars, x = "wt", y = "mpg", add = "reg.line", conf.int = TRUE, color = "cyl", palette = "jco", shape = "cyl")+
  stat_cor(aes(color = cyl), label.x = 3)
# arrange the plots
ggarrange(sp,                                                 # First row with scatter plot
          ggarrange(bxp, dp, ncol = 2, labels = c("B", "C")), # Second row with box and dot plots
          nrow = 2, 
          labels = "A")                                       # Labels of the scatter plot

以这种方式排列图给了我输出。

但是，我希望以另一种方式输出，例如散点图应该位于下窗格中，bx 和 bp 应该位于顶部窗格中。我试过

ggarrange(bxp, dp, ggarrange(sp, labels = c("C"), nrow = 1),
         nrow = 2, ncol = 2, labels=c("A", "B"))

但它给了我如下：

散点图未填充下窗格。它位于窗格的一角

我在文本文件中有一些超链接。我想将第一行上的链接与下一个相邻行进行比较，并根据数字创建链接？。例如，

考虑下面的相邻链接

https://gp.to/ab/394/las69-02-09-2020/
https://gp.to/ab/394/las69-02-09-2020/4/

这里的输出文件将是：

https://gp.to/ab/394/las69-02-09-2020/
https://gp.to/ab/394/las69-02-09-2020/2/
https://gp.to/ab/394/las69-02-09-2020/3/
https://gp.to/ab/394/las69-02-09-2020/4/

同样，我需要对其他线路做同样的事情......

输入示例：

https://gp.to/ab/394/las69-02-09-2020/
https://gp.to/ab/394/las69-02-09-2020/4/
https://gp.to/ab/563/dimp-02-07-2023/
https://gp.to/ab/39443/omegs-02-07-2023/
https://gp.to/ab/39443/omegs-02-07-2023/3/
https://gp.to/ab/39443/lis-22-04-2018/
https://gp.to/ab/39443/lis-22-04-2018/2/
https://gp.to/ab/39443/madi-22-04-2018/
https://gp.to/ab/39443/madi-22-04-2018/5/

输出示例：

https://gp.to/ab/394/las69-02-09-2020/
https://gp.to/ab/394/las69-02-09-2020/2/
https://gp.to/ab/394/las69-02-09-2020/3/
https://gp.to/ab/394/las69-02-09-2020/4/
https://gp.to/ab/563/dimp-02-07-2023/
https://gp.to/ab/39443/omegs-02-07-2023/
https://gp.to/ab/39443/omegs-02-07-2023/2/
https://gp.to/ab/39443/omegs-02-07-2023/3/
https://gp.to/ab/39443/lis-22-04-2018/
https://gp.to/ab/39443/lis-22-04-2018/2/
https://gp.to/ab/39443/madi-22-04-2018/
https://gp.to/ab/39443/madi-22-04-2018/2/
https://gp.to/ab/39443/madi-22-04-2018/3/
https://gp.to/ab/39443/madi-22-04-2018/4/
https://gp.to/ab/39443/madi-22-04-2018/5/

我试过..

# Function to extract the number from a URL
def extract_number(url):
    parts = url.split('/')
    for part in parts[::-1]:
        if part.isdigit():
            return int(part)
    return None

# Read the input file
with open('input.txt', 'r') as input_file:
    lines = input_file.readlines()

output_lines = []

# Iterate through the input lines and generate output lines
for i in range(len(lines)):
    current_url = lines[i].strip()
    output_lines.append(current_url)

    if i + 1 < len(lines):
        next_url = lines[i + 1].strip()
        current_number = extract_number(current_url)
        next_number = extract_number(next_url)

        if current_number is not None and next_number is not None:
            for num in range(current_number + 1, next_number):
                new_url = current_url.rsplit('/', 1)[0] + '/' + str(num) + '/'
                output_lines.append(new_url)

# Write the output to a file
with open('output.txt', 'w') as output_file:
    output_file.writelines(output_lines)

但我没有得到想要的输出。