@@ -11,6 +11,8 @@ The package includes
11
11
12
12
* Normality check (Shapiro Wilk test)
13
13
14
+ * Volcano plot
15
+
14
16
* Heatmap
15
17
16
18
* PERMANOVA
@@ -176,11 +178,38 @@ write.csv(Result,"Normality_test_Result.csv")
176
178
<img src =" https://user-images.githubusercontent.com/77651662/126578553-f2d583db-d649-4db7-92bb-8cfa9433904a.PNG " width =" 400 " height =" 350 " >
177
179
</p >
178
180
181
+ ### Volcano plot
182
+
183
+ ```
184
+ # Makes a subdirectory and saves Volcano plots for different combination of groups
185
+ Test<-Allstats(Data)
186
+ Volcano(Test,asterisk = "t-test")
187
+ ```
188
+ <p align =" center " >
189
+ <img src =" https://user-images.githubusercontent.com/77651662/127811109-0cb273ba-3c01-4679-9cb3-c510f3176592.png " width =" 400 " height =" 400 " >
190
+ <img src =" https://user-images.githubusercontent.com/77651662/127811667-980ee12e-ec12-4786-98b9-22b4c027f5c1.png " width =" 400 " height =" 400 " >
191
+ </p >
179
192
180
193
194
+ ##### Adjustable parameters
195
+
196
+ * asterisk = "t-test" #statistics inheriting from Allstats "Scheffe", "t-test", "u-test", "Dunn"
197
+ * reverse = T # T, F reverse the direction of fold change
198
+ * fig_width = NA #figure size
199
+ * fig_height = NA #figure size
200
+ * FC_log = 2 # Fold change log transformation value
201
+ * pval_log = 10 #p_value log transformation value
202
+ * dotsize = 3 #dotsize
203
+ * x_limit = c(-2,2) #x axis limt
204
+ * y_limit =c(0,6) #y axis limit
205
+ * pval_intercept = 0.05 # intercept for identification
206
+ * sig_label = T # T,F label significant variables
207
+ * color=c("#FF3300","#FF6600","#FFCC00") colors used for ggplots.
181
208
### Heatmap
182
209
183
210
```
211
+ # Makes a subdirectory and saves Heatmap
212
+
184
213
scaled_data<-D_tran(Data,param = "Auto")
185
214
186
215
AS_heatmap(scaled_data) #data inheriting from D_tran
0 commit comments