{"id":462,"date":"2023-05-10T11:57:54","date_gmt":"2023-05-10T11:57:54","guid":{"rendered":"https:\/\/yunshangtulv.com.cn\/?p=462"},"modified":"2023-05-10T11:57:54","modified_gmt":"2023-05-10T11:57:54","slug":"sci%e5%9b%be%e7%89%87%e5%a4%8d%e7%8e%b0%ef%bc%9a%e7%83%ad%e5%9b%be%e6%9f%b1%e7%8a%b6%e5%9b%be","status":"publish","type":"post","link":"https:\/\/yunshangtulv.com.cn\/?p=462","title":{"rendered":"SCI\u56fe\u7247\u590d\u73b0\uff1a\u70ed\u56fe+\u67f1\u72b6\u56fe"},"content":{"rendered":"<p><span>\u521b\u5efa\u4e00\u4e2a\u5305\u542b5\u79cd\u80bf\u7624\u7c7b\u578b\uff08A, B, C, D, E\uff09\u548c10\u4e2a\u57fa\u56e0\uff08Gene1\u5230Gene10\uff09\u7684\u6570\u636e\u96c6\uff0c\u6bcf\u4e2a\u57fa\u56e0\u5728\u6bcf\u79cd\u80bf\u7624\u7c7b\u578b\u4e2d\u7684\u51fa\u73b0\u9891\u7387\u662f\u968f\u673a\u751f\u6210\u7684<\/span><\/p>\n<pre class=\"corepress-code-pre\"><code>library(xlsx)\r\nlibrary(ComplexHeatmap)\r\nlibrary(tidyverse)\r\nlibrary(ggplot2)\r\nlibrary(circlize)\r\nlibrary(patchwork)\r\nlibrary(ggplotify)\r\n\r\n\r\n# \u751f\u6210\u865a\u6784\u6570\u636e\r\nset.seed(123) # \u8bbe\u7f6e\u968f\u673a\u79cd\u5b50\u4ee5\u4fbf\u7ed3\u679c\u53ef\u91cd\u73b0\r\nfake_data &lt;- data.frame(\r\n  Gene = rep(paste0(\"Gene\", 1:10), 5),\r\n  `Abbreviation.of.Tumor.Type` = rep(LETTERS[1:5], each = 10),\r\n  Freq = sample(1:15, 50, replace = TRUE)\r\n)\r\n\r\n# \u663e\u793a\u524d\u51e0\u884c\u6570\u636e\r\nhead(fake_data)\r\n\r\n\r\n\r\nlength(data$Gene)\r\nlength(data$`Abbreviation.of.Tumor.Type`)\r\n\r\n\r\n# \u6570\u636e\u9884\u5904\u7406\uff1a\r\ndata_mat &lt;- fake_data %&gt;%\r\n  pivot_wider(names_from = `Abbreviation.of.Tumor.Type`, values_from = Freq) %&gt;%\r\n  column_to_rownames(\"Gene\")\r\n\r\ndata_mat &lt;- data_mat[,order(colSums(data_mat), decreasing = TRUE)]\r\ndata_mat &lt;- data_mat[order(rowSums(data_mat), decreasing = TRUE),]\r\ndata_mat2 &lt;- as.matrix(data_mat)\r\ndata_mat2[which(data_mat2 == 0)] &lt;- NA\r\n\r\n# \u4fee\u6539\u989c\u8272\u548c\u6dfb\u52a0\u56fe\u4f8b\u3001\u6587\u5b57\u6ce8\u91ca\u3001\u63cf\u8fb9\r\ncol_fun = colorRamp2(c(0, 5, 10, 15), c(\"#b4d9e5\", \"#91a1cf\", \"#716bbf\",\"#5239a3\"))\r\n\r\n# \u521b\u5efa\u70ed\u56fe\r\nheatmap_plot &lt;- Heatmap(data_mat2,\r\n                        col = col_fun,\r\n                        na_col = \"white\",\r\n                        cluster_rows = F,\r\n                        cluster_columns = F,\r\n                        row_names_side = \"left\",\r\n                        heatmap_legend_param = list(\r\n                          title = \"Frequency(%)\",\r\n                          title_position = \"leftcenter\",\r\n                          legend_direction = \"horizontal\"\r\n                        ),\r\n                        row_names_gp = gpar(fontsize = 10, font = 3),\r\n                        column_names_gp = gpar(fontsize = 10, font = 3),\r\n                        cell_fun = function(j, i, x, y, width, height, fill) {\r\n                          if (!is.na(data_mat2[i, j])) {\r\n                            grid.text(sprintf(\"%1.f\", data_mat2[i, j]), x, y,\r\n                                      gp = gpar(fontsize = 10, col = \"#df9536\"))\r\n                            grid.rect(x, y, width, height,\r\n                                      gp = gpar(col = \"grey\", fill = NA, lwd = 0.8))\r\n                          }\r\n                        })\r\n\r\n# \u4fdd\u5b58\u70ed\u56fe\u4e3aPDF\r\npdf(\"Heatmap.pdf\", height = 8, width = 8)\r\ndraw(heatmap_plot, heatmap_legend_side = \"bottom\")\r\ndev.off()\r\n\r\n\r\n\r\n\r\n# \u521b\u5efa\u5806\u79ef\u67f1\u72b6\u56fe\r\nstacked_bar_data &lt;- as_tibble(data_mat \/ rowSums(data_mat)) %&gt;%\r\n  pivot_longer(cols = everything(), names_to = \"CancerType\",\r\n               values_to = \"value\")\r\nstacked_bar_data$Gene &lt;- factor(rep(rownames(data_mat), each = 5), \r\n                                levels = rev(rownames(data_mat)))\r\n\r\nstacked_bar_plot &lt;- ggplot(stacked_bar_data) +\r\n  geom_bar(aes(x = Gene, y = value, fill = CancerType), \r\n           position = \"stack\", stat = \"identity\") +\r\n  scale_y_continuous(labels = seq(0, 1, 0.25), position = \"right\") +\r\n  ggsci::scale_fill_igv() +\r\n  ylab(\"Percentage(%)\") +\r\n  theme_bw() +\r\n  theme(panel.grid = element_blank(), \r\n        axis.title.y = element_blank(),\r\n        axis.text.y = element_blank(),\r\n        axis.ticks.y = element_blank(),\r\n        axis.title.x = element_text(face = \"bold\"),\r\n        legend.position = \"bottom\",\r\n        legend.key.size = unit(0.3, 'cm'),\r\n        legend.title=element_text(face=\"bold\")) +\r\n  labs(fill = \"Tumor Type\") +\r\n  guides(fill = guide_legend(title.position = \"top\",\r\n                             title.hjust = 0.5, ncol = 2, \r\n                             byrow = TRUE)) +\r\n  coord_flip()\r\n\r\nstacked_bar_plot\r\n\r\n# \u4fdd\u5b58\u5806\u79ef\u67f1\u72b6\u56fe\u4e3aPDF\r\nggsave(\"Stacked_Barplot.pdf\", plot = stacked_bar_plot, height = 8, width = 1.5)\r\n\r\n\r\n# \u5c06\u70ed\u56fe\u8f6c\u6362\u4e3a ggplot \u5bf9\u8c61\r\nheatmap_ggplot &lt;- as.ggplot(heatmap_plot, heatmap_legend_side = \"bottom\")\r\n\r\n# \u5408\u5e76\u4e24\u4e2a\u56fe\u5f62\r\ncombined_plot &lt;- heatmap_ggplot + stacked_bar_plot + plot_layout(ncol = 2, widths = c(3, 1))\r\n\r\n# \u663e\u793a\u5408\u5e76\u540e\u7684\u56fe\u5f62\r\ncombined_plot\r\n\r\n# \u4fdd\u5b58\u5408\u5e76\u540e\u7684\u56fe\u5f62\u4e3a PDF\r\nggsave(\"Combined_Plot.pdf\", plot = combined_plot, height = 8, width = 9.5)\r\n<\/code><\/pre>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<p><img decoding=\"async\" src=\"https:\/\/yunshangtulv.com.cn\/wp-content\/uploads\/2023\/05\/1683719795608.webp\" \/><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u521b\u5efa\u4e00\u4e2a\u5305\u542b5\u79cd\u80bf\u7624\u7c7b\u578b\uff08A, B, C, D, E\uff09\u548c10\u4e2a\u57fa\u56e0\uff08Gene1\u5230Gene10\uff09\u7684\u6570\u636e\u96c6\uff0c\u6bcf\u4e2a\u57fa [&hellip;]<\/p>\n","protected":false},"author":111,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[9],"tags":[],"class_list":["post-462","post","type-post","status-publish","format-standard","hentry","category-r"],"_links":{"self":[{"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/posts\/462","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/users\/111"}],"replies":[{"embeddable":true,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=462"}],"version-history":[{"count":0,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=\/wp\/v2\/posts\/462\/revisions"}],"wp:attachment":[{"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=462"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=462"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/yunshangtulv.com.cn\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=462"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}