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我有一张大桌子，可以在这里作为Renvironment使用，它看起来像这样：

基因 s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 类型
电车2 0 0 0 0 0 0 0 0 0 0 0 0 蛋白质编码
CLIC5 0 0 1 0 1 0.2 0 0 1.3 1 0 0.7 蛋白质编码
GAL3ST2 0 0.5 0 0 0 0 0 0 0 0 0 0 特纳
超高频1BP 0 0 0 0 0 0 0 0 0 0 0 0 特纳
OSTM1 0 0 0 0 0 0 0 0 0 0 0 0 特纳
IMPG2 0 0 0 1 0 0 0 0 0 0 0 0 小RNA
OXCT1 0 1 0 0 0 0 0 0 0 0 0 0.3 小RNA
CPNE3 0 0 0 0 0 0 0 0 0 0 0 0 小RNA
PPP1R15 0 0 0 0 0 0 0 0 0 0 0 0 小RNA
亚当11 0 0 0 0 0 0 0 0 0 0 0 0 snoRNA
PTHLH 0 0 0 0 0.1 0.5 0 0 0.1 0.2 0 0.5 snoRNA

通过使用以下代码，我可以获得所有单元格的唯一元素 OF TYPE（最后一列）“

table <-read.delim("smalRNAseq/counts_molc_NoLengthCut_mirnaCollapsed2.txt", header = T, sep = "\t")
genecodev22 <-read.table("genecodev22.csv")

#assign new names to the coluns so I can merge them
colnames(genecodev22)[colnames(genecodev22) %in% c("V1", "V2")] <- c("ENSEMBLE", "TYPE")
colnames(table)[colnames(table) %in% c("X", "X.1")] <- c("ENSEMBLE1", "ENSEMBLE")
#mergethem by ENSEMBLE so that the type will be a new entry at the back
mergetable <- merge(table,genecodev22, match = "first", by="ENSEMBLE")
#assign the first column as column names, the one with the true ensemble names
row.names(mergetable) <- mergetable[[1]]
#and remove it
mergetable2 <- mergetable[,-2:-1]
#get all entries with no 0 value
mergetable3 <- mergetable2[rowSums(mergetable2[1:nrow(mergetable2),1:95])>0,]
# Total number of unique element and occurancy p
list_of_elements <- aggregate(data.frame(count = mergetable3$TYPE),
                              list(value = mergetable3$TYPE),
                              length)
#plot it
row.names(list_of_elements) <- list_of_elements[[1]]
list_of_elements <- list_of_elements[-1]
list_of_elementsOrd<- list_of_elements[order(list_of_elements$count, decreasing = T),]
library(ggplot2)
ggplot(as.data.frame(list_of_elementsOrd),
       aes(x=reorder(value, -count), y=count, fill=value)) +
       geom_bar(stat = "identity") +
       coord_flip() +
       geom_text(aes(label=count), vjust=-1, color="black", size=3.5)+
      theme(axis.text.x = element_text(angle = 90), legend.position = "none")

输出如下所示： 在此处输入图像描述

我想要什么我 希望每个 s# 绘制一个堆叠箱形图，其具有唯一的类型（不应该计算 0）。

非常感谢

编辑：我设法使用以下循环创建所有“聚合”元素的列表：

i=1
list_of_elementsOrd <- c()
mergedElements <- list_of_elements[1:2]
for (i in 1:length(mergetable2[-1])) {
  function(row) all(row !=0 )), ] 
  mergetable2[mergetable2 == 0] <- NA
  list_of_elements <- aggregate(data.frame(count = mergetable2$TYPE),
                                list(value = mergetable2$TYPE),
                                length)
  list_of_elementsOrd[[i]]<- list_of_elements[order(list_of_elements$count, decreasing = T),]
  }

但我当然无法完成剧情。当我将其转换为数据框时，我得到 column_names 为：

value.70 count.70                value.71 count.71
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1 回答 1

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您可以将所有 0 替换为NA，因此堆叠的条形图不应包含带有 NA 的基因。

为此：

table[table == 0] <- NA
于 2021-06-29T20:42:51.463 回答