diff --git a/R_decontaminer_visualizationScript/barPlotInfo_ge_CT_5_breast.txt b/R_decontaminer_visualizationScript/barPlotInfo_ge_CT_5_breast.txt
new file mode 100644
index 0000000..f69e693
--- /dev/null
+++ b/R_decontaminer_visualizationScript/barPlotInfo_ge_CT_5_breast.txt
@@ -0,0 +1,299 @@
+	Breast-03	Breast-08	Breast-100	Breast-10	Breast-15	Breast-16	Breast-21	Breast-33	Breast-42	Breast-454	Breast-48	Breast-50	Breast-55	Breast-564	Breast-56	Breast-590	Breast-59	Breast-603	Breast-60	Breast-61	Breast-85	Breast-86	Breast-97	Breast-ALK-82	Breast-H11	Breast-H31	Breast-H38	Breast-H59	Breast-H63	Breast-H66	Breast-H68	Breast-H74	Breast-H75	Breast-H76	Breast-H81	Breast-H83	Breast-H84	Breast-H89	Breast-H92
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+Acinetobacter	0	29.17656374	13.97058824	11.11111111	3.284671533	11.95087388	41.77877429	7.191624943	0	7.228915663	24.17251755	3.333333333	6.52446675	0	2.728731942	32.98969072	8.481421648	0	7.662835249	28.40909091	5.813953488	0	1.338582677	0	0	0	1.711652403	0	6.25	1.540522438	1.351351351	1.524390244	0	1.054481547	0	0	0	0.867381876	7.603635558
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+Rugamonas	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Ruminococcus	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Saccharopolyspora	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Salmonella	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Sanguibacter	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Sanguibacteroides	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Serratia	0	0.197941409	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.726978998	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Shewanella	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Simonsiella	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Sneathia	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Sphingobacterium	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Sphingobium	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.802568218	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.433690938	0
+Sphingomonas	6.382978723	0.989707047	0	8.333333333	2.189781022	1.606046292	1.569506726	0.910332271	0	0	2.106318957	6.222222222	1.756587202	0	7.704654896	0	2.504038772	0	0	3.896103896	0	0	3.307086614	0	0	4.672897196	0	0	5.208333333	0	0.45045045	0	0	0.263620387	0	0	0	0.479342616	0.266016404
+Sphingopyxis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Spirosoma	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Staphylococcus	5.673758865	2.929532858	0	18.05555556	6.569343066	18.80018895	3.512705531	9.285389167	4.761904762	6.024096386	3.7111334	6.222222222	11.16687578	38.0952381	5.778491172	6.18556701	5.169628433	1.325757576	11.87739464	4.87012987	0	7.788944724	9.212598425	10.37037037	0	29.90654206	7.175773535	2.032520325	13.54166667	13.596785	7.477477477	4.87804878	0	8.875219684	45.22968198	9.803921569	24.13793103	4.199954348	4.610951009
+Stenotrophomonas	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.266016404
+Streptococcus	3.191489362	2.137767221	41.91176471	3.472222222	8.394160584	2.92867265	2.092675635	3.186162949	13.60544218	30.12048193	2.507522568	3.777777778	3.262233375	0	1.926163724	18.55670103	7.754442649	1.325757576	6.513409962	1.298701299	6.976744186	4.522613065	5.984251969	5.925925926	9.574468085	21.4953271	2.040816327	0	32.29166667	0.803750837	4.054054054	7.012195122	0	3.9543058	0	0	0	2.670623145	2.194635336
+Streptomyces	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Sulfurihydrogenibium	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Tannerella	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.540540541	0	0	0	0	0	0	0	0
+Tepidimonas	0	0	0	0	4.379562044	0	0	0.910332271	0	0	0	0	0	0	1.76565008	0	0.646203554	0	15.3256705	0	0	0	0.787401575	0	0	0	0	0	0	0	0	0	0	0.219683656	0	0	0	9.564026478	0
+Tepidiphilus	4.255319149	1.108471892	0	0	2.189781022	0	0.971599402	1.502048248	0	0	0	0	2.885821832	0	3.531300161	0	0	0	0	1.461038961	0	0	3.385826772	0	0	0	0.329163924	0	0	0	0	0	0	0	0	0	0	1.369550331	0
+Tessaracoccus	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Tetragenococcus	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Thauera	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Thermoanaerobacterium	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.502168455	0
+Thermomonas	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.551181102	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.136955033	0
+Thermorudis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Thermus	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5.748031496	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Thioclava	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Tropicimonas	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Trueperella	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Tsukamurella	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Turicella	0	0.237529691	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4.020100503	0	0	0	7.476635514	0.394996708	0	0	0	0	1.829268293	0	0.834797891	0	0	0	0.273910066	0.376856573
+Ureaplasma	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Varibaculum	0	0	0	0	0	0.283419934	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Variovorax	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Veillonella	0	0	0	0	0	0	0	0.227583068	0	0	4.012036108	0	0	0	0	0	0	0	0	0	0	0	0.551181102	0	0	0	0	5.284552846	0	0	0.540540541	0	0	0	0	0	0	0	0.155176236
+Vibrio	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Williamsia	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Xanthomonas	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.399024607
+Xylophilus	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
\ No newline at end of file
diff --git a/R_decontaminer_visualizationScript/decontaminer.R b/R_decontaminer_visualizationScript/decontaminer.R
new file mode 100644
index 0000000..c4d0805
--- /dev/null
+++ b/R_decontaminer_visualizationScript/decontaminer.R
@@ -0,0 +1,99 @@
+### set working directory and load input file 
+
+setwd("test_html/")
+originaldata <- read.table("barPlotInfo_ge_CT_5_breast.txt",sep='\t', row.names=1, header=TRUE) ## should be data frame
+
+### select sub set based on coulmn number or name 
+
+ newdata_1=subset(originaldata, select=c(1:10,22,23))  ## col number based OR
+ #newdata_1=subset(originaldata, select=c("Breast.03","Breast.08","Breast.100")) ##name based
+
+############# Mean greater than threshold ####################
+newdata_1=newdata_1[rowSums(newdata_1) >0.1 ,drop=FALSE, ] #take only those rows which are greater than zero
+
+## apply filter all sample threshold
+allsample_threshhold <- 1
+data_wt=newdata_1[(rowSums(newdata_1)/nrow(newdata_1))>= allsample_threshhold,drop=FALSE, ]
+nor <- data_wt
+data_wt <- as.data.frame(t(data_wt))
+
+
+library(tidyverse)
+library('dplyr') ##HAS COUNT FUNCTION
+
+## preparation of data format for plots
+data_wt$Sample <-  row.names(data_wt)  
+data_wt <- data_wt %>% 
+  pivot_longer(!Sample, names_to = "Species", values_to = "count") # Gathering the columns to have normalized counts to a single column
+
+
+####  Lets Plot #################
+library(ggplot2)
+library(RColorBrewer)
+
+## setting 2 different color variables
+
+my_palette <- colorRampPalette(c("#179493","#76c286", "#ebdc96", "#ec9173","#d0587e"), alpha=TRUE)(n=20)
+heat_colors <- brewer.pal(6, "Reds") ##"Greens"  ##"Blues"
+
+#####  First : Stack plot with count #### 
+
+ggplot(data_wt, aes(x = Sample, y = count, fill = Species)) + 
+  geom_bar(stat = "identity")  + theme(axis.text.x = element_text(angle = 60, vjust = 1, hjust=1))
+
+#####  Second : Stack plot with percent #### 
+
+ggplot(data_wt, aes(x = Sample, y = count, fill = Species)) + 
+  geom_col(position = "fill") +
+  scale_y_continuous(labels = scales::percent)  + theme(axis.text.x = element_text(angle = 60, vjust = 1, hjust=1))
+
+#### Third :Dot Plot (Sample vs Species with count size)  ##########
+
+ggplot(data_wt,aes(x=Species,y=Sample )) +
+  geom_point(aes(size=count,  color = Species))+
+  scale_color_manual(values = heat_colors )+              ### in case heat_color doesnt work replace with manual or other like c("red","blue")
+  #scale_color_gradientn('Log2 mean (Molecule 1, Molecule 2)', colors=my_palette) +
+  ggtitle("Sample vs Species with count size ") +
+  theme_bw() +
+  theme(panel.grid.minor = element_blank(),
+        panel.grid.major = element_blank(),
+        axis.text=element_text(size=14, colour = "black"),
+        axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),
+        axis.text.y = element_text(size=12, colour = "black"),
+        axis.title=element_blank(),
+        panel.border = element_rect(size = 0.5, linetype = "solid", colour = "black"))
+
+
+
+#######  Fourth : Dot Plot (Sample vs Count)
+
+ggplot(data_wt) +
+  geom_point(aes(x = Sample , y = count, color = Species )) +
+  ## scale_y_log10() +  ##want to scale it or not??
+  xlab("Sample ID") +
+  ylab("Counts") +
+  ggtitle("Sample vs Count") +
+  theme_bw() +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
+  theme(plot.title = element_text(hjust = 0.5))
+
+
+
+################  Fifth : Heat Map ##############3
+
+library(ComplexHeatmap)
+### Run pheatmap
+pheatmap::pheatmap( nor, 
+                    color = my_palette, 
+                    cluster_cols  = T,
+                    cluster_rows = F,
+                    show_rownames = T,
+                    border_color = NA, 
+                    fontsize = 10, 
+                    scale = "row", #row #column #none  ## row wise differences clarity (i.e b/w samples)
+                    fontsize_row = 10, 
+                    height = 20, 
+                    main= "Heat map (Sample level differences)"
+)
+
+
diff --git a/R_decontaminer_visualizationScript/decontaminer.Rmd b/R_decontaminer_visualizationScript/decontaminer.Rmd
new file mode 100644
index 0000000..0fd83a9
--- /dev/null
+++ b/R_decontaminer_visualizationScript/decontaminer.Rmd
@@ -0,0 +1,124 @@
+---
+title: "Decontaminer Visualization support"
+author: "Amarinder Singh Thind"
+date: "2022 Dec 07"
+output:
+  html_document:
+    toc: yes
+    code_folding: hide
+  pdf_document:
+    toc: yes
+---
+### set working directory and load input file 
+
+```{r}
+setwd("test_html/")
+originaldata <- read.table("barPlotInfo_ge_CT_5_breast.txt",sep='\t', row.names=1, header=TRUE) ## should be data frame
+```
+
+### select sub set based on coulmn number or name 
+
+```{r}
+
+
+ newdata_1=subset(originaldata, select=c(1:10,22,23))  ## col number based OR
+ #newdata_1=subset(originaldata, select=c("Breast.03","Breast.08","Breast.100")) ##name based
+```
+
+#### Mean greater than threshold ####################
+
+```{r}
+
+newdata_1=newdata_1[rowSums(newdata_1) >0.1 ,drop=FALSE, ] #take only those rows which are greater than zero
+
+allsample_threshhold <- 1 ## Define threshold for average count > threshold
+
+data_wt=newdata_1[(rowSums(newdata_1)/nrow(newdata_1))>= allsample_threshhold,drop=FALSE, ]
+nor <- data_wt
+data_wt <- as.data.frame(t(data_wt))
+```
+
+## preparation of data format for plots
+```{r}
+library(tidyverse)
+library('dplyr') ##HAS COUNT FUNCTION
+
+data_wt$Sample <-  row.names(data_wt)  
+data_wt <- data_wt %>% 
+  pivot_longer(!Sample, names_to = "Species", values_to = "count") # Gathering the columns to have normalized counts to a single column
+```
+
+####  Lets Plot #################
+```{r}
+library(ggplot2)
+library(RColorBrewer)
+
+## setting 2 different color variables
+
+my_palette <- colorRampPalette(c("#179493","#76c286", "#ebdc96", "#ec9173","#d0587e"), alpha=TRUE)(n=20)
+heat_colors <- brewer.pal(6, "Reds") ##"Greens"  ##"Blues"
+```
+
+#####  First : Stack plot with count #### 
+
+```{r}
+ggplot(data_wt, aes(x = Sample, y = count, fill = Species)) + 
+  geom_bar(stat = "identity")  + theme(axis.text.x = element_text(angle = 60, vjust = 1, hjust=1))
+```
+
+#####  Second : Stack plot with percent #### 
+```{r}
+ggplot(data_wt, aes(x = Sample, y = count, fill = Species)) + 
+  geom_col(position = "fill") +
+  scale_y_continuous(labels = scales::percent)  + theme(axis.text.x = element_text(angle = 60, vjust = 1, hjust=1))
+```
+
+#### Third :Dot Plot (Sample vs Species with count size)  ##########
+```{r}
+ggplot(data_wt,aes(x=Species,y=Sample )) +
+  geom_point(aes(size=count,  color = Species))+
+  scale_color_manual(values = heat_colors )+              ### in case heat_color doesnt work replace with manual or other like c("red","blue")
+  #scale_color_gradientn('Log2 mean (Molecule 1, Molecule 2)', colors=my_palette) +
+  ggtitle("Sample vs Species with count size ") +
+  theme_bw() +
+  theme(panel.grid.minor = element_blank(),
+        panel.grid.major = element_blank(),
+        axis.text=element_text(size=14, colour = "black"),
+        axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),
+        axis.text.y = element_text(size=12, colour = "black"),
+        axis.title=element_blank(),
+        panel.border = element_rect(size = 0.5, linetype = "solid", colour = "black"))
+```
+
+#####  Fourth : Dot Plot (Sample vs Count)
+```{r}
+ggplot(data_wt) +
+  geom_point(aes(x = Sample , y = count, color = Species )) +
+  ## scale_y_log10() +  ##want to scale it or not??
+  xlab("Sample ID") +
+  ylab("Counts") +
+  ggtitle("Sample vs Count") +
+  theme_bw() +
+  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
+  theme(plot.title = element_text(hjust = 0.5))
+
+```
+
+####  Fifth : Heat Map ##############3
+```{r}
+library(ComplexHeatmap)
+### Run pheatmap
+pheatmap::pheatmap( nor, 
+                    color = my_palette, 
+                    cluster_cols  = T,
+                    cluster_rows = F,
+                    show_rownames = T,
+                    border_color = NA, 
+                    fontsize = 10, 
+                    scale = "row", #row #column #none  ## row wise differences clarity (i.e b/w samples)
+                    fontsize_row = 10, 
+                    height = 20, 
+                    main= "Heat map (Sample level differences)"
+)
+
+```