In mikeod38/dauergut: Scripts for rict-1 dauer paper
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(message = FALSE)
knitr::opts_chunk$set(warning = FALSE)
pathname = here::here()
library(magrittr)
library(knitr)
library(dplyr)
library(ggplot2)
library(ggbeeswarm)
library(beeswarm)
library(ggthemes)
library(viridis)
library(lme4)
library(schoRsch)
library(DHARMa)
library(multcomp)
library(tidyr)
library(rstanarm)
library(ggrepel)
library(rstan)
library(rstanarm)
library(MASS)
devtools::install_github("mikeod38/dauergut")
library(dauergut)
library(plotly)
library(lsmeans)
dauer_ANOVA <- . %>% lm(data = ., formula = pct ~ genotype)
Intestinal mTORC2 alters foraging behaviors{.tabset}
4A-B
img.path <- file.path(pathname, "figures","4A_cartoon.png")
``` {r, results = 'markup', eval = TRUE}
include_graphics(img.path)
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**Figure 4B**
_rict-1_ acts in the intestine to regulate foraging behavior. Foraging is increased in _rict-1_ mutants, which is rescued using the intestine-specific _ges-1_ promoter. Plot shows exploratory behavior of indicated strains. Each purple dot represents data from a single worm. Median is indicated by a horizontal purple line; error bars are quartiles. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the total number of animals examined during 3 independent days of assays. P-values shown are between indicated values; `***` and `***` - different from WT and rict-1 at P<0.001, respectively (GLMM with Tukey-type multivariate-t post-hoc adjustment). P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively.
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##4C-D
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**Figure 4C**
Live tracking of foraging behavior. Shown is a representative assay. n > 20 animals per assay. Density plot shows mean speed and angular velocity from tracks binned over 10 sec intervals imaged at 3 frames/sec. Red line indicates delineation of roaming (upper region) and dwelling (lower region) behavior.
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**Figure 4D**
Quantification of roaming and dwelling states. _rict-1_ mutants show increased roaming, corresponding to an odds ratio of `r round(odds.ratio,3)`. Dots show proportion of track time bins in which animals were roaming, with each dot reflecting one assay. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. P-value shown is with respect to wild-type (Welch’s t-test).
##4E
pdfr-1 is epistatic to rict-1 in foraging behavior.
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**Figure 4E**
TORC2 requires PDFR-1 neuropeptide signaling to modulate foraging behavior. Exploratory behavior of indicated strains. Each purple dot represents data from a single worm. Median is indicated by a horizontal purple line; error bars are quartiles. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the total number of animals examined during 3 independent days of assays. P-values shown are between indicated values; `***` and `***` - different from WT and rict-1 at P<0.001, respectively (GLMM with Tukey-type multivariate-t post-hoc adjustment). P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively.
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##4F
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**Figure 4F**
PDF-2 signaling acts downstream of TORC2 in the regulation of foraging. Overexpression of _pdf-2_ specifically suppresses the _rict-1_ foraging defect. Exploratory behavior of indicated strains is shown. Each purple dot represents data from a single worm. Median is indicated by a horizontal purple line; error bars are quartiles. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the total number of animals examined during 3 independent days of assays. A single _pdf-1p::pdf-2_ transgene was examined. P-values shown are between indicated values; `***` and `^^^` - different from WT and rict-1 at P<0.001, respectively (GLMM with Tukey-type multivariate-t post-hoc adjustment). P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively.
##S2A-B
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**Figure S2A-B**
(left) Live tracking of foraging behavior in starved worms. Shown is a representative assay. n > 20 animals per assay. Density plot shows mean speed and angular velocity from tracks binned over 10 sec intervals imaged at 3 frames/sec. Red line indicates delineation of roaming and dwelling behavior. (right) Quantification of roaming and dwelling states. Dots show proportion of track time bins in which animals were roaming, with each dot reflecting one assay. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. P-value shown is with respect to wild-type (Welch’s t-test).
##S2C
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**Figure S2C**
pdfr-1 mutations do not suppress rict-1 dauer formation phenotypes. Each dot indicates the average number of dauers formed in a single assay. Horizontal bar indicates median. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the number of independent assays with at least 27 animals each. P-value shown in comparison to rict-1 mutants.
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mikeod38/dauergut documentation built on May 30, 2019, 7:16 p.m.
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knitr::opts_chunk$set(echo = TRUE) knitr::opts_chunk$set(message = FALSE) knitr::opts_chunk$set(warning = FALSE) pathname = here::here() library(magrittr) library(knitr) library(dplyr) library(ggplot2) library(ggbeeswarm) library(beeswarm) library(ggthemes) library(viridis) library(lme4) library(schoRsch) library(DHARMa) library(multcomp) library(tidyr) library(rstanarm) library(ggrepel) library(rstan) library(rstanarm) library(MASS) devtools::install_github("mikeod38/dauergut") library(dauergut) library(plotly) library(lsmeans) dauer_ANOVA <- . %>% lm(data = ., formula = pct ~ genotype)
Intestinal mTORC2 alters foraging behaviors{.tabset}
4A-B
img.path <- file.path(pathname, "figures","4A_cartoon.png")
``` {r, results = 'markup', eval = TRUE}
include_graphics(img.path)
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**Figure 4B** _rict-1_ acts in the intestine to regulate foraging behavior. Foraging is increased in _rict-1_ mutants, which is rescued using the intestine-specific _ges-1_ promoter. Plot shows exploratory behavior of indicated strains. Each purple dot represents data from a single worm. Median is indicated by a horizontal purple line; error bars are quartiles. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the total number of animals examined during 3 independent days of assays. P-values shown are between indicated values; `***` and `***` - different from WT and rict-1 at P<0.001, respectively (GLMM with Tukey-type multivariate-t post-hoc adjustment). P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively. wzxhzdk:5 ##4C-D wzxhzdk:6
**Figure 4D** Quantification of roaming and dwelling states. _rict-1_ mutants show increased roaming, corresponding to an odds ratio of `r round(odds.ratio,3)`. Dots show proportion of track time bins in which animals were roaming, with each dot reflecting one assay. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. P-value shown is with respect to wild-type (Welch’s t-test). ##4E pdfr-1 is epistatic to rict-1 in foraging behavior. wzxhzdk:10 wzxhzdk:11 **Figure 4E** TORC2 requires PDFR-1 neuropeptide signaling to modulate foraging behavior. Exploratory behavior of indicated strains. Each purple dot represents data from a single worm. Median is indicated by a horizontal purple line; error bars are quartiles. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the total number of animals examined during 3 independent days of assays. P-values shown are between indicated values; `***` and `***` - different from WT and rict-1 at P<0.001, respectively (GLMM with Tukey-type multivariate-t post-hoc adjustment). P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively. wzxhzdk:12 ##4F wzxhzdk:13 wzxhzdk:14 **Figure 4F** PDF-2 signaling acts downstream of TORC2 in the regulation of foraging. Overexpression of _pdf-2_ specifically suppresses the _rict-1_ foraging defect. Exploratory behavior of indicated strains is shown. Each purple dot represents data from a single worm. Median is indicated by a horizontal purple line; error bars are quartiles. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the total number of animals examined during 3 independent days of assays. A single _pdf-1p::pdf-2_ transgene was examined. P-values shown are between indicated values; `***` and `^^^` - different from WT and rict-1 at P<0.001, respectively (GLMM with Tukey-type multivariate-t post-hoc adjustment). P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively. ##S2A-B wzxhzdk:15
**Figure S2C** pdfr-1 mutations do not suppress rict-1 dauer formation phenotypes. Each dot indicates the average number of dauers formed in a single assay. Horizontal bar indicates median. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the number of independent assays with at least 27 animals each. P-value shown in comparison to rict-1 mutants. wzxhzdk:20
mikeod38/dauergut documentation built on May 30, 2019, 7:16 p.m.
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**Figure 4B** _rict-1_ acts in the intestine to regulate foraging behavior. Foraging is increased in _rict-1_ mutants, which is rescued using the intestine-specific _ges-1_ promoter. Plot shows exploratory behavior of indicated strains. Each purple dot represents data from a single worm. Median is indicated by a horizontal purple line; error bars are quartiles. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the total number of animals examined during 3 independent days of assays. P-values shown are between indicated values; `***` and `***` - different from WT and rict-1 at P<0.001, respectively (GLMM with Tukey-type multivariate-t post-hoc adjustment). P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively. wzxhzdk:5 ##4C-D wzxhzdk:6
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**Figure 4C**
Live tracking of foraging behavior. Shown is a representative assay. n > 20 animals per assay. Density plot shows mean speed and angular velocity from tracks binned over 10 sec intervals imaged at 3 frames/sec. Red line indicates delineation of roaming (upper region) and dwelling (lower region) behavior.
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**Figure 4D** Quantification of roaming and dwelling states. _rict-1_ mutants show increased roaming, corresponding to an odds ratio of `r round(odds.ratio,3)`. Dots show proportion of track time bins in which animals were roaming, with each dot reflecting one assay. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. P-value shown is with respect to wild-type (Welch’s t-test). ##4E pdfr-1 is epistatic to rict-1 in foraging behavior. wzxhzdk:10 wzxhzdk:11 **Figure 4E** TORC2 requires PDFR-1 neuropeptide signaling to modulate foraging behavior. Exploratory behavior of indicated strains. Each purple dot represents data from a single worm. Median is indicated by a horizontal purple line; error bars are quartiles. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the total number of animals examined during 3 independent days of assays. P-values shown are between indicated values; `***` and `***` - different from WT and rict-1 at P<0.001, respectively (GLMM with Tukey-type multivariate-t post-hoc adjustment). P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively. wzxhzdk:12 ##4F wzxhzdk:13 wzxhzdk:14 **Figure 4F** PDF-2 signaling acts downstream of TORC2 in the regulation of foraging. Overexpression of _pdf-2_ specifically suppresses the _rict-1_ foraging defect. Exploratory behavior of indicated strains is shown. Each purple dot represents data from a single worm. Median is indicated by a horizontal purple line; error bars are quartiles. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the total number of animals examined during 3 independent days of assays. A single _pdf-1p::pdf-2_ transgene was examined. P-values shown are between indicated values; `***` and `^^^` - different from WT and rict-1 at P<0.001, respectively (GLMM with Tukey-type multivariate-t post-hoc adjustment). P-values of differences in means relative to wild-type and corresponding mutant animals are indicated in black and red, respectively. ##S2A-B wzxhzdk:15
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**Figure S2A-B**
(left) Live tracking of foraging behavior in starved worms. Shown is a representative assay. n > 20 animals per assay. Density plot shows mean speed and angular velocity from tracks binned over 10 sec intervals imaged at 3 frames/sec. Red line indicates delineation of roaming and dwelling behavior. (right) Quantification of roaming and dwelling states. Dots show proportion of track time bins in which animals were roaming, with each dot reflecting one assay. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. P-value shown is with respect to wild-type (Welch’s t-test).
##S2C
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**Figure S2C** pdfr-1 mutations do not suppress rict-1 dauer formation phenotypes. Each dot indicates the average number of dauers formed in a single assay. Horizontal bar indicates median. Light gray thin and thick vertical bars at right indicate Bayesian 95% and 75% credible intervals, respectively. Numbers in parentheses below indicate the number of independent assays with at least 27 animals each. P-value shown in comparison to rict-1 mutants. wzxhzdk:20
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.