| title | author | date | output | ||||
|---|---|---|---|---|---|---|---|
Viral Comparison: Group Project |
Aryss Hearne |
3/6/2021 |
|
Hypothesis: Viruses that target land plants will exhibit higher gene load and higher genome lengths than viruses that target humans.
library(tidyverse)## -- Attaching packages --------------------------------------- tidyverse 1.3.0 --
## v ggplot2 3.3.3 v purrr 0.3.4
## v tibble 3.1.0 v dplyr 1.0.4
## v tidyr 1.1.2 v stringr 1.4.0
## v readr 1.4.0 v forcats 0.5.1
## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()
library(here)## here() starts at C:/Users/starf/Documents/GitHub/Bis15LBuds
library(janitor)##
## Attaching package: 'janitor'
## The following objects are masked from 'package:stats':
##
## chisq.test, fisher.test
virus<-readr::read_csv("data/viruses.csv")##
## -- Column specification --------------------------------------------------------
## cols(
## `Organism Name` = col_character(),
## `Organism Groups` = col_character(),
## BioSample = col_logical(),
## BioProject = col_character(),
## Assembly = col_character(),
## Level = col_character(),
## `Size(Mb)` = col_double(),
## `GC%` = col_double(),
## Host = col_character(),
## CDS = col_double(),
## Neighbors = col_double(),
## `Release Date` = col_datetime(format = ""),
## `GenBank FTP` = col_character(),
## `RefSeq FTP` = col_character(),
## Genes = col_double(),
## Scaffolds = col_double()
## )
## Warning: 344 parsing failures.
## row col expected actual file
## 1438 BioSample 1/0/T/F/TRUE/FALSE SAMN02981359 'data/viruses.csv'
## 4401 BioSample 1/0/T/F/TRUE/FALSE SAMN02981224 'data/viruses.csv'
## 8940 BioSample 1/0/T/F/TRUE/FALSE SAMN01137200 'data/viruses.csv'
## 8941 BioSample 1/0/T/F/TRUE/FALSE SAMN01137212 'data/viruses.csv'
## 8944 BioSample 1/0/T/F/TRUE/FALSE SAMN01137140 'data/viruses.csv'
## .... ......... .................. ............ ..................
## See problems(...) for more details.
virus## # A tibble: 34,747 x 16
## `Organism Name` `Organism Groups` BioSample BioProject Assembly Level
## <chr> <chr> <lgl> <chr> <chr> <chr>
## 1 White spot syndrom~ Viruses;Other;Nimav~ NA <NA> GCA_0008~ Comp~
## 2 Posavirus sp. Viruses;unclassifie~ NA <NA> GCA_0023~ Comp~
## 3 Hepatitis E virus Viruses;Other;Hepev~ NA <NA> GCA_0008~ Comp~
## 4 Heterosigma akashi~ Viruses;Other;Marna~ NA <NA> GCA_0008~ Comp~
## 5 Pyrococcus abyssi ~ Viruses;unclassifie~ NA <NA> GCA_0008~ Comp~
## 6 Marine RNA virus S~ Viruses;Other;Other NA <NA> GCA_0008~ Comp~
## 7 Tomato marchitez v~ Viruses;Other;Secov~ NA <NA> GCA_0008~ Comp~
## 8 Ourmia melon virus Viruses;Other;Botou~ NA <NA> GCA_0008~ Comp~
## 9 Epirus cherry virus Viruses;Other;Botou~ NA <NA> GCA_0008~ Comp~
## 10 Vibrio phage dougl~ Viruses;Other;Podov~ NA PRJNA39215 GCA_0009~ Comp~
## # ... with 34,737 more rows, and 10 more variables: Size(Mb) <dbl>, GC% <dbl>,
## # Host <chr>, CDS <dbl>, Neighbors <dbl>, Release Date <dttm>,
## # GenBank FTP <chr>, RefSeq FTP <chr>, Genes <dbl>, Scaffolds <dbl>
virus$Host<-as.factor(virus$Host)
levels(virus$Host)## [1] "algae"
## [2] "archaea"
## [3] "bacteria"
## [4] "bacteria,fungi,human,invertebrates"
## [5] "bacteria,human"
## [6] "bacteria,human,invertebrates,land plants,protozoa"
## [7] "bacteria,human,vertebrates"
## [8] "diatom"
## [9] "eukaryotic algae"
## [10] "eukaryotic algae,human,invertebrates,vertebrates"
## [11] "fungi"
## [12] "fungi,invertebrates"
## [13] "fungi,vertebrates"
## [14] "human"
## [15] "human,invertebrates"
## [16] "human,invertebrates,vertebrates"
## [17] "human,vertebrates"
## [18] "invertebrates"
## [19] "invertebrates, vertebrates"
## [20] "invertebrates,land plants"
## [21] "invertebrates,vertebrates"
## [22] "land plants"
## [23] "plants"
## [24] "protozoa"
## [25] "vertebrates"
## [26] "vertebrates, human"
virus_c<-virus%>%
separate('Host', into=c("host_type_1", "host_type_2", "host_type_3"), sep=",")## Warning: Expected 3 pieces. Additional pieces discarded in 637 rows [1198,
## 10504, 15643, 15930, 16037, 16487, 17027, 17209, 17261, 17262, 17299, 17422,
## 17712, 17811, 17840, 17841, 17867, 17945, 18145, 18215, ...].
## Warning: Expected 3 pieces. Missing pieces filled with `NA` in 28898 rows [1, 2,
## 3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, ...].
virus_c## # A tibble: 34,747 x 18
## `Organism Name` `Organism Groups` BioSample BioProject Assembly Level
## <chr> <chr> <lgl> <chr> <chr> <chr>
## 1 White spot syndrom~ Viruses;Other;Nimav~ NA <NA> GCA_0008~ Comp~
## 2 Posavirus sp. Viruses;unclassifie~ NA <NA> GCA_0023~ Comp~
## 3 Hepatitis E virus Viruses;Other;Hepev~ NA <NA> GCA_0008~ Comp~
## 4 Heterosigma akashi~ Viruses;Other;Marna~ NA <NA> GCA_0008~ Comp~
## 5 Pyrococcus abyssi ~ Viruses;unclassifie~ NA <NA> GCA_0008~ Comp~
## 6 Marine RNA virus S~ Viruses;Other;Other NA <NA> GCA_0008~ Comp~
## 7 Tomato marchitez v~ Viruses;Other;Secov~ NA <NA> GCA_0008~ Comp~
## 8 Ourmia melon virus Viruses;Other;Botou~ NA <NA> GCA_0008~ Comp~
## 9 Epirus cherry virus Viruses;Other;Botou~ NA <NA> GCA_0008~ Comp~
## 10 Vibrio phage dougl~ Viruses;Other;Podov~ NA PRJNA39215 GCA_0009~ Comp~
## # ... with 34,737 more rows, and 12 more variables: Size(Mb) <dbl>, GC% <dbl>,
## # host_type_1 <chr>, host_type_2 <chr>, host_type_3 <chr>, CDS <dbl>,
## # Neighbors <dbl>, Release Date <dttm>, GenBank FTP <chr>, RefSeq FTP <chr>,
## # Genes <dbl>, Scaffolds <dbl>
virus_c$host_type_1<-as.factor(virus_c$host_type_1)
virus_c$host_type_2<-as.factor(virus_c$host_type_2)
virus_c$host_type_3<-as.factor(virus_c$host_type_3)
levels(virus_c$host_type_1)## [1] "algae" "archaea" "bacteria" "diatom"
## [5] "eukaryotic algae" "fungi" "human" "invertebrates"
## [9] "land plants" "plants" "protozoa" "vertebrates"
levels(virus_c$host_type_2)## [1] " human" " vertebrates" "fungi" "human"
## [5] "invertebrates" "land plants" "vertebrates"
levels(virus_c$host_type_3)## [1] "human" "invertebrates" "vertebrates"
virus_clong<-virus_c%>%
pivot_longer(host_type_1:host_type_3,
names_to="host_num",
values_to="host_type",
values_drop_na=T)
virus_clong## # A tibble: 42,108 x 17
## `Organism Name` `Organism Groups` BioSample BioProject Assembly Level
## <chr> <chr> <lgl> <chr> <chr> <chr>
## 1 White spot syndr~ Viruses;Other;Nimavi~ NA <NA> GCA_00084~ Comp~
## 2 Posavirus sp. Viruses;unclassified~ NA <NA> GCA_00237~ Comp~
## 3 Hepatitis E virus Viruses;Other;Hepevi~ NA <NA> GCA_00086~ Comp~
## 4 Hepatitis E virus Viruses;Other;Hepevi~ NA <NA> GCA_00086~ Comp~
## 5 Pyrococcus abyss~ Viruses;unclassified~ NA <NA> GCA_00087~ Comp~
## 6 Tomato marchitez~ Viruses;Other;Secovi~ NA <NA> GCA_00087~ Comp~
## 7 Ourmia melon vir~ Viruses;Other;Botour~ NA <NA> GCA_00087~ Comp~
## 8 Epirus cherry vi~ Viruses;Other;Botour~ NA <NA> GCA_00087~ Comp~
## 9 Vibrio phage dou~ Viruses;Other;Podovi~ NA PRJNA39215 GCA_00090~ Comp~
## 10 Vibrio phage hel~ Viruses;Other;Myovir~ NA PRJNA39217 GCA_00090~ Comp~
## # ... with 42,098 more rows, and 11 more variables: Size(Mb) <dbl>, GC% <dbl>,
## # CDS <dbl>, Neighbors <dbl>, Release Date <dttm>, GenBank FTP <chr>,
## # RefSeq FTP <chr>, Genes <dbl>, Scaffolds <dbl>, host_num <chr>,
## # host_type <fct>
virus_clean<-virus_clong%>%
separate('Organism Groups', into=c("domain", "kingdom", "subgroup"), sep=";")%>%
filter(Level=="Complete" & (host_type=="human" | host_type=="land plants"))%>%
select('host_type', 'Organism Name', 'kingdom','subgroup', 'Size(Mb)', 'GC%', 'Genes','Level')%>%
rename(organism_name='Organism Name', kingdom=kingdom, subgroup=subgroup, level="Level", size_mb='Size(Mb)', perc_gc='GC%', host=host_type, genes_num='Genes')%>%
arrange(host)
virus_clean## # A tibble: 11,871 x 8
## host organism_name kingdom subgroup size_mb perc_gc genes_num level
## <fct> <chr> <chr> <chr> <dbl> <dbl> <dbl> <chr>
## 1 human Hepatitis E virus Other Hepeviridae 0.00718 57.9 3 Compl~
## 2 human Salivirus NG-J1 Other Picornavir~ 0.00798 56.7 1 Compl~
## 3 human Astrovirus VA1 Other Astrovirid~ 0.00659 41.9 3 Compl~
## 4 human Pseudocowpox virus Other Poxviridae 0.145 65 134 Compl~
## 5 human Torque teno mini ~ Other Anelloviri~ 0.00291 37.8 2 Compl~
## 6 human Torque teno virus~ Other Anelloviri~ 0.00373 53.4 4 Compl~
## 7 human Torque teno virus~ Other Anelloviri~ 0.00377 51.2 4 Compl~
## 8 human Torque teno virus~ Other Anelloviri~ 0.00374 48.4 3 Compl~
## 9 human Torque teno virus~ Other Anelloviri~ 0.00375 51.4 6 Compl~
## 10 human Torque teno virus~ Other Anelloviri~ 0.00376 53.8 3 Compl~
## # ... with 11,861 more rows
virus_clean%>%
select(size_mb)%>%
summary()## size_mb
## Min. :0.000248
## 1st Qu.:0.001768
## Median :0.007496
## Mean :0.012225
## 3rd Qu.:0.017433
## Max. :0.232608
virus_clean%>%
ggplot(aes(x=size_mb, fill=host, color=kingdom))+
geom_histogram(alpha=0.25)+
scale_y_log10()## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Transformation introduced infinite values in continuous y-axis
## Warning: Removed 195 rows containing missing values (geom_bar).
library(shiny)
library(shinydashboard)##
## Attaching package: 'shinydashboard'
## The following object is masked from 'package:graphics':
##
## box