{"id":27727,"date":"2024-02-02T16:23:19","date_gmt":"2024-02-02T08:23:19","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27727"},"modified":"2024-02-02T16:23:21","modified_gmt":"2024-02-02T08:23:21","slug":"ccplotr-%e5%8f%af%e8%a7%86%e5%8c%96%e7%bb%86%e8%83%9e%e9%97%b4%e7%9b%b8%e4%ba%92%e4%bd%9c%e7%94%a8%ef%bc%88scrna-seq%ef%bc%89","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=27727","title":{"rendered":"CCPlotR: \u53ef\u89c6\u5316\u7ec6\u80de\u95f4\u76f8\u4e92\u4f5c\u7528\uff08scRNA-seq\uff09"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u8981\u5206\u4eab\u7684\u65b0\u9c9c\u597d\u5305\u662f2023\u5e749\u670820\u65e5<\/strong>\u53d1\u8868\u4e8eBioinformatics Advances<\/em>\u4e0a\u7528\u4e8e\u53ef\u89c6\u5316\u7ec6\u80de\u95f4\u76f8\u4e92\u4f5c\u7528\u7684CCplotR\uff01<\/p>\n

\"fig:\"<\/p>\n

\u5728\u751f\u7269\u4fe1\u606f\u5b66\u9886\u57df\uff0c\u7814\u7a76\u7ec6\u80de\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u5bf9\u4e8e\u7406\u89e3\u590d\u6742\u7684\u751f\u7269\u5b66\u8fc7\u7a0b\u81f3\u5173\u91cd\u8981\u3002\u4e3a\u4e86\u5e2e\u52a9\u5c0f\u4f19\u4f34\u4eec\u66f4\u597d\u5730\u5206\u6790\u548c\u53ef\u89c6\u5316\u8fd9\u4e9b\u76f8\u4e92\u4f5c\u7528\uff0c\u5c0f\u679c\u5411\u5927\u5bb6\u4ecb\u7ecd\u8fd9\u4e00\u6b3e\u540d\u4e3aCCPlotR\u7684R\u5305\u3002\u5b83\u4e13\u4e3a\u5904\u7406\u548c\u53ef\u89c6\u5316\u4ece\u5355\u7ec6\u80de\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u9884\u6d4b\u51fa\u7684\u7ec6\u80de\u95f4\u76f8\u4e92\u4f5c\u7528\u800c\u8bbe\u8ba1\uff0c\u53ea\u9700\u8f93\u5165\u9884\u6d4b\u7684\u4ea4\u4e92\u4f5c\u7528\u8868\u5373\u53ef\u751f\u6210\u4e00\u7cfb\u5217\u5b8c\u6574\u7684\u3001\u53ef\u7528\u4e8e\u53d1\u8868\u7684\u56fe\u5f62\uff0c\u5982\u70ed\u56fe\u3001\u70b9\u56fe\u3001\u73af\u5f62\u56fe\u548c\u7f51\u7edc\u56fe\u7b49\u3002\u5bf9\u4e8e\u4ece\u4e8b\u7ec6\u80de\u95f4\u76f8\u4e92\u4f5c\u7528\u7814\u7a76\u7684\u5c0f\u4f19\u4f34\u4eec\u6765\u8bf4\uff0cCCPlotR\u65e0\u7591\u662f\u4e00\u6b3e\u975e\u5e38\u5b9e\u7528\u7684\u5de5\u5177\u3002<\/p>\n

CCPlotR\u53ef\u4ee5\u753b\u51fa\u591a\u79cd\u7c7b\u578b\u7684\u56fe\uff0c\u7528\u4e8e\u53ef\u89c6\u5316\u6765\u81eaLiana\u3001CellPhoneDB\u3001NATMI\u7b49\u591a\u4e2a\u5de5\u5177\u7684\u7ed3\u679c\u3002\u6240\u9700\u8f93\u5165\u4ec5\u4e3a\u4e00\u4e2a\u5305\u542b\u201csource\u201d\u3001\u201ctarget\u201d\u3001\u201cligand\u201d\u3001\u201creceptor\u201d\u548c\u201cscore\u201d\u8fd9\u4e9b\u5217\u7684DataFrame\u3002\u5e94\u7c7b\u4f3c\u4e8e\u4ee5\u4e0b\u5f62\u5f0f\uff1a<\/p>\n\n\n\n\n\n\n\n\n\n\n
source<\/th>\n<\/tr>\n<\/thead>\n
B<\/td>\n<\/tr>\n
B<\/td>\n<\/tr>\n
CD8 T<\/td>\n<\/tr>\n
B<\/td>\n<\/tr>\n
NK<\/td>\n<\/tr>\n
B<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

\u5bf9\u4e8e\u67d0\u4e9b\u56fe\uff0c\u8fd8\u53ef\u4ee5\u9009\u62e9\u663e\u793a\u6bcf\u79cd\u7ec6\u80de\u7c7b\u578b\u4e2d\u7684\u914d\u4f53\u548c\u53d7\u4f53\u7684\u8868\u8fbe\u3002\u5bf9\u4e8e\u8fd9\u4e9b\u56fe\uff0c\u9700\u8981\u7b2c\u4e8c\u4e2a\u6570\u636e\u6846\uff0c\u5b83\u5305\u542b\u6bcf\u79cd\u7ec6\u80de\u7c7b\u578b\u4e2d\u6bcf\u4e2a\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u503c\uff0c\u770b\u8d77\u6765\u5e94\u8be5\u50cf\u8fd9\u6837\uff1a<\/p>\n\n\n\n\n\n\n\n\n\n\n
cell_type<\/th>\n<\/tr>\n<\/thead>\n
B<\/td>\n<\/tr>\n
B<\/td>\n<\/tr>\n
B<\/td>\n<\/tr>\n
B<\/td>\n<\/tr>\n
B<\/td>\n<\/tr>\n
B<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

\u8be5\u5305\u9644\u5e26\u793a\u4f8b\u6570\u636e\u96c6(‘toy_data’\uff0c ‘toy_exp’)\uff0c\u5927\u5bb6\u53ef\u4ee5\u770b\u770b~<\/p>\n

\u5b89\u88c5<\/h2>\n

\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u547d\u4ee4\u6765\u5b89\u88c5R\u5305\uff1a<\/p>\n

# install development version
\ndevtools::install_github(“Sarah145\/CCPlotR”)<\/p>\n

# or install from Bioconductor
\nif (!requireNamespace(“BiocManager”, quietly = TRUE)) {
\ninstall.packages(“BiocManager”)
\n}<\/p>\n

BiocManager::install(“CCPlotR”)<\/p>\n

\u53ef\u89c6\u5316\u7c7b\u578b<\/h2>\n

\u8be5\u5305\u5305\u542b\u7528\u4e8e\u751f\u6210\u516d\u79cd\u7c7b\u578b\u7684\u56fe\u7684\u51fd\u6570\uff1acc_heatmap\uff0ccc_dotplot\uff0ccc_network\uff0ccc_circos\uff0ccc_arrow\u548ccc_sigmoid\u3002\u4e0b\u9762\u662f\u6bcf\u79cd\u56fe\u5f62\u7c7b\u578b\u7684\u4e00\u4e9b\u793a\u4f8b\u3002<\/p>\n

\u70ed\u56fe\uff08cc_heatmap\uff09<\/h3>\n

\u6b64\u51fd\u6570\u53ef\u4ee5\u751f\u6210\u56db\u79cd\u4e0d\u540c\u6837\u5f0f\u7684\u70ed\u56fe\u3002\u9009\u9879A\u4ec5\u663e\u793a\u6bcf\u5bf9\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u603b\u6570\uff0c\u800c\u9009\u9879B\u663e\u793a\u53c2\u4e0e\u6bcf\u4e2a\u76f8\u4e92\u4f5c\u7528\u7684\u914d\u4f53\u3001\u53d7\u4f53\u548c\u7ec6\u80de\u7c7b\u578b\u4ee5\u53ca\u5b83\u4eec\u7684\u5206\u6570\u3002\u4e3a\u4e86\u907f\u514d\u56fe\u5f62\u6df7\u4e71\uff0c\u9009\u9879B\u4ec5\u663e\u793a\u4e00\u5c0f\u90e8\u5206\u6700\u76f8\u5173\u7684\u76f8\u4e92\u4f5c\u7528\u3002\u8fd8\u6709\u4e00\u9879\u9009\u9879\uff0c\u4ee5CellPhoneDB\u548cLiana\u7b49\u6d41\u884c\u7684\u7ec6\u80de\u95f4\u76f8\u4e92\u4f5c\u7528\u9884\u6d4b\u5de5\u5177\u7684\u98ce\u683c\u751f\u6210\u70ed\u56fe\u3002<\/p>\n

library(CCPlotR)
\ndata(toy_data, toy_exp, package = ‘CCPlotR’)
\ncc_heatmap(toy_data)
\ncc_heatmap(toy_data, option = ‘B’, n_top_ints = 10)
\ncc_heatmap(toy_data, option = ‘CellPhoneDB’)<\/p>\n

\"fig:\"<\/p>\n

\u70b9\u56fe\uff08cc_dotplot\uff09<\/h3>\n

\u8be5\u51fd\u6570\u53ef\u4ee5\u751f\u6210\u56db\u79cd\u4e0d\u540c\u6837\u5f0f\u7684\u70b9\u56fe\u3002\u9009\u9879A\u4ec5\u663e\u793a\u6bcf\u79cd\u7ec6\u80de\u7c7b\u578b\u5bf9\u4e4b\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u603b\u6570\uff0c\u800c\u9009\u9879B\u663e\u793a\u53c2\u4e0e\u6bcf\u79cd\u76f8\u4e92\u4f5c\u7528\u7684\u914d\u4f53\u3001\u53d7\u4f53\u548c\u7ec6\u80de\u7c7b\u578b\u4ee5\u53ca\u5b83\u4eec\u7684\u76f8\u4e92\u4f5c\u7528\u5206\u6570\u3002\u4e3a\u907f\u514d\u56fe\u5f62\u6df7\u4e71\uff0c\u5728\u9009\u9879B\u4e2d\u4ec5\u663e\u793a\u4e00\u5c0f\u90e8\u5206\u9ad8\u76f8\u4e92\u4f5c\u7528\u3002\u6b64\u5916\uff0c\u8fd8\u6709\u4e00\u79cd\u9009\u9879\u53ef\u4ee5\u751f\u6210\u7c7b\u4f3c\u4e8e\u5e7f\u53d7\u6b22\u8fce\u7684\u7ec6\u80de\u95f4\u76f8\u4e92\u4f5c\u7528\u9884\u6d4b\u5de5\u5177CellPhoneDB\u548cLiana\u7684\u70b9\u56fe\u6837\u5f0f\u3002<\/p>\n

cc_dotplot(toy_data)
\ncc_dotplot(toy_data, option = ‘B’, n_top_ints = 10)
\ncc_dotplot(toy_data, option = ‘Liana’, n_top_ints = 15)<\/p>\n

\"fig:\"<\/p>\n

\u7f51\u7edc\uff08cc_network\uff09<\/h3>\n

\u6b64\u51fd\u6570\u53ef\u4ee5\u751f\u6210\u4e24\u79cd\u4e0d\u540c\u7c7b\u578b\u7f51\u7edc\u56fe\u3002\u5728\u9009\u9879A\u4e2d\uff0c\u8282\u70b9\u4ee3\u8868\u7ec6\u80de\u7c7b\u578b\uff0c\u8fb9\u6743\u91cd\u5bf9\u5e94\u4e8e\u7ed9\u5b9a\u7ec6\u80de\u7c7b\u578b\u5bf9\u4e4b\u95f4\u7684\u603b\u4ea4\u4e92\u6570\u3002\u5728\u9009\u9879B\u4e2d\uff0c\u8282\u70b9\u662f\u914d\u4f53\u548c\u53d7\u4f53\u57fa\u56e0\uff0c\u4f9d\u636e\u8868\u8fbe\u5b83\u4eec\u7684\u7ec6\u80de\u7c7b\u578b\u8fdb\u884c\u7740\u8272\u3002\u5bf9\u4e8e\u9009\u9879B\uff0c\u4ec5\u663e\u793a\u5c11\u91cf\u6700\u76f8\u5173\u7684\u4ea4\u4e92\u4f5c\u7528\u4ee5\u907f\u514d\u56fe\u5f62\u6df7\u4e71\u3002<\/p>\n

cc_network(toy_data)
\ncc_network(toy_data, colours = c(‘orange’, ‘cornflowerblue’, ‘hotpink’), option = ‘B’)<\/p>\n

\"fig:\"<\/p>\n

\u5f26\u56fe (cc_circos)<\/h3>\n

\u8be5\u51fd\u6570\u53ef\u4ee5\u751f\u6210\u4e09\u79cd\u4e0d\u540c\u7c7b\u578b\u7684\u5f26\u56fe\u3002\u9009\u9879A\u751f\u6210\u4e00\u4e2a\u5f26\u56fe\uff0c\u5176\u4e2d\u94fe\u63a5\u7684\u5bbd\u5ea6\u8868\u793a\u6bcf\u79cd\u7ec6\u80de\u7c7b\u578b\u5bf9\u4e4b\u95f4\u7684\u603b\u76f8\u4e92\u4f5c\u7528\u6b21\u6570\u3002\u9009\u9879B\u751f\u6210\u4e00\u4e2a\u5f26\u56fe\uff0c\u663e\u793a\u4e86\u76f8\u4e92\u4f5c\u7528\u9876\u90e8\u5206\u6d89\u53ca\u7684\u914d\u4f53\u3001\u53d7\u4f53\u548c\u7ec6\u80de\u7c7b\u578b\u3002\u9009\u9879C\u6269\u5927\u4e86\u9009\u9879B\u7684\u5185\u5bb9\uff0c\u8fd8\u663e\u793a\u4e86\u6bcf\u79cd\u7ec6\u80de\u7c7b\u578b\u4e2d\u914d\u4f53\u548c\u53d7\u4f53\u57fa\u56e0\u7684\u5e73\u5747\u8868\u8fbe\u6c34\u5e73\u3002\u5728\u9009\u9879B\u548c\u9009\u9879C\u4e2d\uff0c\u94fe\u63a5\u7684\u6743\u91cd\u8868\u793a\u76f8\u4e92\u4f5c\u7528\u7684\u5f97\u5206\u3002<\/p>\n

cc_circos(toy_data)
\ncc_circos(toy_data, option = ‘B’, n_top_ints = 10)
\ncc_circos(toy_data, option = ‘C’, n_top_ints = 15, exp_df = toy_exp, cell_cols = c(`B` = ‘hotpink’, `NK` = ‘orange’, `CD8 T` = ‘cornflowerblue’), palette = ‘PuRd’)<\/p>\n

\"fig:\"<\/p>\n

\u5bf9\u7bad\u5934\u56fe\uff08cc_arrow\uff09<\/h3>\n

\u6b64\u51fd\u6570\u751f\u6210\u663e\u793a\u7ed9\u5b9a\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u76f8\u4e92\u4f5c\u7528\u7684\u56fe\u8868\u3002\u9009\u9879A\u4ec5\u663e\u793a\u4e00\u5bf9\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u76f8\u4e92\u4f5c\u7528\u7684\u914d\u4f53\/\u53d7\u4f53\uff0c\u800c\u9009\u9879B\u8fd8\u663e\u793a\u6bcf\u4e2a\u7ec6\u80de\u7c7b\u578b\u4e2d\u914d\u4f53\/\u53d7\u4f53\u57fa\u56e0\u7684\u8868\u8fbe\u60c5\u51b5\u3002\u5728\u8fd9\u4e24\u4e2a\u9009\u9879\u4e2d\uff0c\u7bad\u5934\u7684\u7c97\u7ec6\u4ee3\u8868\u76f8\u4e92\u4f5c\u7528\u7684\u5206\u6570\u3002<\/p>\n

cc_arrow(toy_data, cell_types = c(‘B’, ‘CD8 T’), colours = c(`B` = ‘hotpink’, `CD8 T` = ‘orange’))
\ncc_arrow(toy_data, cell_types = c(‘NK’, ‘CD8 T’), option = ‘B’, exp_df = toy_exp, n_top_ints = 10, palette = ‘OrRd’)<\/p>\n

\"fig:\"<\/p>\n

Sigmoid\u56fe\uff08cc_sigmoid\uff09<\/h3>\n

\u6b64\u51fd\u6570\u4f7f\u7528ggbump R\u5305\u4e2d\u7684geom_sigmoid\u51fd\u6570\u7ed8\u5236\u90e8\u5206\u76f8\u4e92\u4f5c\u7528\uff0c\u5c06\u53d1\u9001\u7ec6\u80de\u4e2d\u7684\u914d\u4f53\u4e0e\u63a5\u6536\u7ec6\u80de\u4e2d\u7684\u53d7\u4f53\u8fde\u63a5\u8d77\u6765\u3002<\/p>\n

cc_sigmoid(toy_data)<\/p>\n

\"fig:\"<\/p>\n

\u53c2\u8003\u6587\u732e<\/h2>\n

[1] Sarah Ennis, Pilib \u00d3 Broin, Eva Szegezdi, CCPlotR: an R package for the visualization of cell\u2013cell interactions, Bioinformatics Advances<\/em>, Volume 3, Issue 1, 2023, vbad130, https:\/\/doi.org\/10.1093\/bioadv\/vbad130<\/a><\/p>\n

\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u4f7f\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\u4e3a\uff1a(http:\/\/www.biocloudservice.com\/home.html<\/a>)\uff0c\u5176\u4e2d\u4e5f\u5305\u62ec\u4e86\u901a\u8def\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/313\/313.php<\/a>)\uff0c\u5355\u7ec6\u80de\u7684\u57fa\u56e0\u5171\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/906\/906.php<\/a>)\u7b49\u5404\u79cd\u5c0f\u5de5\u5177\u54e6~\uff0c\u6709\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u767b\u5f55\u7f51\u7ad9\u8fdb\u884c\u4e86\u89e3\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

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