关于富集分析

[WPFPF]

visCluster(object = cm,

•        plotType = "both",
  

•        column_names_rot = 45,
  

•        showRowNames = F,
  

•        markGenes = markGenes,
  

•        markGenesSide = "left",
  

•        genesGp = c('italic',fontsize = 12,col = "black"),
  

•        annoTermData = enrich,
  

•        lineSide = "left",
  

•        goCol = rep(ggsci::pal_d3()(8),each = 5),
  

•        goSize = "pval")
  

错误于textbox_grob(text = x[[1]], gp = gpar(col = col, fontsize = fontsize, :
参数没有用(wordWrap = TRUE, addNewLine = TRUE)

[podlca22]

same problem

[podlca22]

问题可能出现在visCluster()调用的ComplexHeatmap 中anno_textbox的参数传递上:
textbox <- ComplexHeatmap::anno_textbox(align_to2,
term.list, wordWrap = wordWrap, addNewLine = addNewLine,
side = annoTermMside, background_gp = grid::gpar(fill = termAnnoArg[1],
col = termAnnoArg[2]), by = byGo)

ComplexHeatmap 里面用的是add_new_line = FALSE, word_wrap = FALSE：
textbox_grob(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre",
gp = gpar(), background_gp = gpar(col = "black", fill = "transparent"), round_corners = FALSE, r = unit(0.1, "snpc"),
line_space = unit(4, "pt"), text_space = unit(4, "pt"), max_width = unit(100, "mm"),
padding = unit(4, "pt"), first_text_from = "top", add_new_line = FALSE, word_wrap = FALSE)

不知道把visCluster()代码中的 wordWrap 改成 word_wrap 以及 addNewLine 改成 add_new_line 是否可以修复？

[podlca22]

#152 (comment)

果真是这个原因。把visCluster()复制修改后可以正常运行了。可能是ComplexHeatmap的新版本把参数名称换了。
麻烦作者做出相应的修改并更新版本。

[junjunlab]

目前正在上传bioconductor，还在更新修改，等稳定后使用手册也会进行修改，感谢大家的支持！