使用R为条形图设置一致的x轴间隔

Question

如何获得R来为条形图的x轴输出一致的起点，终点和间隔？ 我有两组数据（矩阵），我想从220开始，在360结束，并且具有相同的刻度线间隔。 绘制图形的目的是轻松比较两个数据集。 所附示例显示了两个图，其中的条形图位于274，但是每个图的比例尺略有不同，因此，条形图没有排列。

这是我正在使用的R代码：

barplot(as.matrix(new_data), ylim = c(0,topmax), ylab = "Reads", 
        col = rainbow(30), cex.lab=1.5, cex.axis=1.5, cex.sub=1.5, col.lab = "blue")
axis(1, seq(220,360))

这是我正在使用的数据矩阵的示例。 假设两个数据集的矩阵相同。

clonename = c("IGH_V4", "IGH_V2", "IGH_V8", "IGH_V7")
readlength = c(456, 654, 457, 345)

P <- matrix(c(0,55,0,65,0,0,4,100,0,0,67,6,0,56,0,0), nrow = 4, byrow = TRUE, dimnames = list(clonename, readlength))
print(P)

提前谢谢你的帮助

Answer 1

我敢肯定有一种方法可以用来处理基本的R图形，这是您用来制作绘图的。 但是，我发现ggplot2软件包使这种事情变得容易得多。 在下面的示例中，我将您提供的数据用作矩阵，然后

library(dplyr) # for mutate and tibble
library(reshape2) # for melt function
library(ggplot2) # for plotting

# Data as you provided
rownames = c("IGH_V4", "IGH_V2", "IGH_V8", "IGH_V7")
colnames = c(456, 654, 457, 345)

reads.m <- matrix(c(0,55,0,65,0,0,4,100,0,0,67,6,0,56,0,0), 
              nrow = 4, byrow = TRUE, 
              dimnames = list(rownames, colnames))

# Melt the matrix into the shape of a dataframe
reads.m <- melt(reads.m)

# Convert the matrix to a data frame (tibble is a type of data frame with
# some nice extra features
reads.df <- as_tibble(reads.m)

# Name the columns
names(reads.df) <- c("Sequence", "Clone", "Reads")

# Create a data frame called diluted with an extra column indicating its
# concentration
diluted.df <- mutate(reads.df, Concentration = "Diluted")

# Do the same for undiluted aka straight then add a clone to change the
# range of clones. Because clones are on the x-axis of your plot, having
# different ranges of data is what presents the problem you're trying to 
# solve by aligning the plot axes.
straight.df <- mutate(reads.df, 
                      Concentration = "Straight",
                      Reads = round(Reads*1.2))
straight.df <- bind_rows(straight.df, tibble(Sequence = NA, 
                                             Clone = 700, 
                                             Reads = 8, 
                                             Concentration = "Straight"))

# Concatenate the tables for the two dilutions.
reads.df <- bind_rows(diluted.df, straight.df)

# Sanity check
print(reads.df, n = nrow(reads.df))

# # A tibble: 33 x 4
# Sequence Clone Reads Concentration
# <fct>    <dbl> <dbl> <chr>        
#   1 IGH_V4     456     0 Diluted      
# 2 IGH_V2     456     0 Diluted      
# 3 IGH_V8     456     0 Diluted      
# 4 IGH_V7     456     0 Diluted      
# 5 IGH_V4     654    55 Diluted      
# 6 IGH_V2     654     0 Diluted      
# 7 IGH_V8     654     0 Diluted      
# 8 IGH_V7     654    56 Diluted      
# 9 IGH_V4     457     0 Diluted      
# 10 IGH_V2     457     4 Diluted      
# 11 IGH_V8     457    67 Diluted      
# 12 IGH_V7     457     0 Diluted      
# 13 IGH_V4     345    65 Diluted      
# 14 IGH_V2     345   100 Diluted      
# 15 IGH_V8     345     6 Diluted      
# 16 IGH_V7     345     0 Diluted      
# 17 IGH_V4     456     0 Straight     
# 18 IGH_V2     456     0 Straight     
# 19 IGH_V8     456     0 Straight     
# 20 IGH_V7     456     0 Straight     
# 21 IGH_V4     654    66 Straight     
# 22 IGH_V2     654     0 Straight     
# 23 IGH_V8     654     0 Straight     
# 24 IGH_V7     654    67 Straight     
# 25 IGH_V4     457     0 Straight     
# 26 IGH_V2     457     5 Straight     
# 27 IGH_V8     457    80 Straight     
# 28 IGH_V7     457     0 Straight     
# 29 IGH_V4     345    78 Straight     
# 30 IGH_V2     345   120 Straight     
# 31 IGH_V8     345     7 Straight     
# 32 IGH_V7     345     0 Straight     
# 33 NA         700     8 Straight     

ggplot(reads.df, aes(x = Clone, y = Reads, fill = Concentration)) +
  geom_col(width = 4) +
  facet_grid(rows = vars(Concentration)) +
  theme_bw() + # White background, rather than default grey
  ylab("Reads")

ggplot(reads.df, aes(x = Clone, y = Reads, fill = Concentration)) +
  geom_col(width = 5) +
  facet_wrap(facets = vars(Concentration)) +
  theme_bw() +  # White background, rather than default grey
  ylab("Reads")

注意：ggplot返回的警告如下所示：

# Warning messages:
# 1: position_stack requires non-overlapping x intervals 
# 2: position_stack requires non-overlapping x intervals 

这是手动设置geom_col宽度的结果。 如果不手动设置该宽度，则列的宽度是如此之窄以至于难以阅读。 使它们变宽不会导致它们重叠，因此我们可以忽略警告。