diff --git a/README.md b/README.md index 5617375..434114b 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,8 @@ The package includes * Normality check (Shapiro Wilk test) +* Volcano plot + * Heatmap * PERMANOVA @@ -176,11 +178,38 @@ write.csv(Result,"Normality_test_Result.csv")

+### Volcano plot + +``` +# Makes a subdirectory and saves Volcano plots for different combination of groups +Test<-Allstats(Data) +Volcano(Test,asterisk = "t-test") +``` +

+ + +

+##### Adjustable parameters + +* asterisk = "t-test" #statistics inheriting from Allstats "Scheffe", "t-test", "u-test", "Dunn" +* reverse = T # T, F reverse the direction of fold change +* fig_width = NA #figure size +* fig_height = NA #figure size +* FC_log = 2 # Fold change log transformation value +* pval_log = 10 #p_value log transformation value +* dotsize = 3 #dotsize +* x_limit = c(-2,2) #x axis limt +* y_limit =c(0,6) #y axis limit +* pval_intercept = 0.05 # intercept for identification +* sig_label = T # T,F label significant variables +* color=c("#FF3300","#FF6600","#FFCC00") colors used for ggplots. ### Heatmap ``` +# Makes a subdirectory and saves Heatmap + scaled_data<-D_tran(Data,param = "Auto") AS_heatmap(scaled_data) #data inheriting from D_tran