added some charts

.Rhistory

@@ -0,0 +1,169 @@
+# 1.1 Pan-cancer expression analysis
+# Load reqquired packages
+library(TCGAplot)
+library(tidyverse)
+gene <- "ITGAX"
+col_pal <- "tron"
+# 1.1.1 Pan-cancer tumor-normal box plot
+pan_boxplot <-  pan_boxplot(gene,
+palette="jco",
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+pan_boxplot
+pan_boxplot(gene,
+palette="jco",
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+# 1.1 Pan-cancer expression analysis
+# Load reqquired packages
+library(TCGAplot)
+library(tidyverse)
+# Input your gene symbol
+gene <- "ITGAX"
+col_pal <- "tron"
+# 1.1.1 Pan-cancer tumor-normal box plot
+pan_boxplot <-  pan_boxplot(gene,
+palette="jco",
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+pan_boxplot
+pan_boxplot(gene,
+palette="lancet",
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+pan_boxplot(gene,
+palette=col_pal,
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+pan_boxplot(gene,
+palette=col_pal,
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+styler:::set_style_transformers()
+ggsave(filename = paste0("figures/01_Pan_cancer_tumor_vs_normal_box_plot/", gene, ".png"),
+plot = pan_boxplot,
+width = 10, height = 6,
+dpi = 300)
+setwd("I://dataviz-gallery/tcga_workflow")
+ggsave(filename = paste0("figures/01_Pan_cancer_tumor_vs_normal_box_plot/", gene, ".png"),
+plot = pan_boxplot,
+width = 10, height = 6,
+dpi = 300)
+ggsave(filename = paste0("figures/01_Pan_cancer_tumor_vs_normal_box_plot/", gene, ".png"),
+plot = pan_boxplot,
+width = 10, height = 6,
+dpi = 300)
+pan_boxplot(gene,
+palette=col_pal,
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+# 1.1.1 Pan-cancer tumor-normal box plot
+pan_boxplot <-  pan_boxplot(gene,
+palette=col_pal,
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+ggsave(filename = paste0("figures/01_Pan_cancer_tumor_vs_normal_box_plot/", gene, ".png"),
+plot = pan_boxplot,
+width = 10, height = 6,
+dpi = 300)
+# Input your gene symbol
+gene <- "PIK31"
+# Input color palette
+# scientific journal palettes from ggsci R package,
+# e.g.: "npg", "aaas", "lancet","tron", "jama", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
+col_pal <- "lancet"
+# 1.1.1 Pan-cancer tumor-normal box plot
+pan_boxplot <-  pan_boxplot(gene,
+palette=col_pal,
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+# Input your gene symbol
+gene <- "PIK3R1"
+# Input color palette
+# scientific journal palettes from ggsci R package,
+# e.g.: "npg", "aaas", "lancet","tron", "jama", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
+col_pal <- "lancet"
+# 1.1.1 Pan-cancer tumor-normal box plot
+pan_boxplot <-  pan_boxplot(gene,
+palette=col_pal,
+legend="right",
+method="wilcox.test") # alternative method "t.test"
+pan_boxplot
+ggsave(filename = paste0("figures/01_Pan_cancer_tumor_vs_normal_box_plot/", gene, ".png"),
+plot = pan_boxplot,
+width = 10, height = 6,
+dpi = 300)
+# 1.1.2. Pan-cancer paired tumor-normal box plot
+pan_paired_boxplot <- pan_paired_boxplot(gene,
+legend = "none",
+palette= col_pal)
+pan_paired_boxplot
+pan_tumor_boxplot <- pan_tumor_boxplot(gene)
+pan_tumor_boxplot
+# 1.2 Pan-caner correction analysis
+# Load required packages
+library(TCGAplot)
+library(tidyverse)
+# Input your gene symbol
+gene <- "PIK3R1"
+gene_TMB_radar(gene, method = "pearson") #The alternatives to be passed to correlation are "spearman" and "kendall".
+gene_MSI_radar(gene,method = "pearson")
+gene <- "PIK3R2"
+# define color gradients
+lowcol <- "#3182bd"
+highcol <- "#f03b20"
+# 1.2.3.1 Pan-cancer gene expression and ICGs correlation
+gene_checkpoint_heatmap <- gene_checkpoint_heatmap(gene,
+method="pearson",
+lowcol= lowcol,highcol= highcol,
+cluster_row=T,cluster_col=T,
+legend=T)
+gene_chemokine_heatmap(gene,
+method="pearson",
+lowcol= lowcol,highcol= highcol,
+cluster_row=T,cluster_col=T,
+legend=T)
+library(TCGAplot)
+library(tidyverse)
+gene <- "WNT11"
+immucell_heatmap <-gene_immucell_heatmap(gene,method="pearson",
+lowcol="blue",highcol="red",
+cluster_row=T,cluster_col=T,legend=T)
+# Input your 2nd gene symbol
+gene<- "WNT2"
+# Input cancer type
+cancer <- "BRCA"
+ROC <- tcga_roc(cancer,gene)
+ROC
+# 3.3.1 Gene-gene correlation scatter
+# Input your 1st gene symbol
+gene1 <- "WNT11"
+gene2 <- "WNT7B"
+# Input cancer type
+cancer <- "BRCA"
+gene_gene_scatter(cancer,gene1,gene2,density="T") # whether density of gene expression was shown.
+# 2.1.1 Expression analysis grouped by clinical information
+library(TCGAplot)
+library(tidyverse)
+# Input your gene symbol
+gene <- "WNT2"
+# Input Cancer type
+cancer<- "BRCA"
+tcga_boxplot(cancer,gene,add = "jitter",
+palette="jco",legend="none",
+label="p.signif",
+method="wilcox.test")
+tcga_boxplot <- tcga_boxplot(cancer,gene,add = "jitter",
+palette="jco",legend="none",
+label="p.signif",
+method="wilcox.test")
+tcga_boxplot
+paired_boxplot(cancer,gene,palette="jco",
+legend="none",label="p.signif",
+method="wilcox.test")
+gene_age(cancer,gene,age=60,
+add = "jitter",palette="jco",
+legend="none",label="p.signif",method="wilcox.test")
+gene_gender(cancer,gene,add = "jitter",
+palette="jco",legend="none",
+label="p.signif",method="wilcox.test")

.Rproj.user/71512E68/pcs/files-pane.pper

@@ -5,5 +5,5 @@
             "ascending": true
         }
     ],
-    "path": "I://dataviz-gallery"
+    "path": "I://dataviz-gallery/reproduce-with-r/figures"
 }

.Rproj.user/71512E68/pcs/windowlayoutstate.pper

@@ -6,7 +6,7 @@
         "windowheight": 983
     },
     "right": {
-        "splitterpos": 589,
+        "splitterpos": 731,
         "topwindowstate": "NORMAL",
         "panelheight": 945,
         "windowheight": 983

.Rproj.user/71512E68/pcs/workbench-pane.pper

@@ -1,5 +1,5 @@
 {
-    "TabSet1": 3,
+    "TabSet1": 4,
     "TabSet2": 4,
     "TabZoom": {}
 }