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Ggplot2

Manufactured by IBM
Sourced in Austria

Ggplot2 is a data visualization package for the R programming language. It provides a powerful and flexible system for creating a wide variety of statistical graphics. Ggplot2 is based on the grammar of graphics, which allows users to build up plots in a layered way. The package offers a consistent interface for manipulating many different types of data.

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3 protocols using ggplot2

1

Microglial Morphology and Density in Brain

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Microglia were detected in free-floating paraformaldehyde-perfused brain tissue by targeting ionized calcium-binding adaptor molecule 1 (rabbit anti-IBA1, 019–19741, Wako, see Supplementary Methods for detailed immunohistochemistry protocol).
Morphological analysis was done at ×10 magnification on a Nikon Eclipse Ni-E microscope. Cell density was obtained by counting the number of IBA1+ cell bodies in the dentate gyrus and cornu ammonis and normalizing to total area, while coverage was measured by dividing the thresholded IBA1 signal by the total area. Microglia in the hilus of the dentate gyrus and the stratum lacunosum-moleculare of the cornu ammonis were classified into five morphological phenotypes as previously described [14 (link), 16 (link), 43 (link)].
After checking for homogeneity of variance and normality, coverage and density data were analyzed using a two-tailed two-way ANOVA, while the morphological subtypes were analyzed with a general linear multivariate model, all using SPSS 25 (IBM software) and graphed using ggplot2 (v3.3.3.9000) [44 ] in R. Data were considered statistically significant when p < 0.05.
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2

Anxiety and Depression Assessment Protocol

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The studied sample was divided into 2 groups to address anxiety and depression, mild and significative symptoms (instead of using the classic grades of none, mild, moderate, moderate-severe, and severe), using a score of 10 as cut point. Continuous variables were represented by mean ± standard deviation and median [interquartile range], and the categorical variables were presented as percentages. To identify the variable distribution type, they were analyzed using the Kolmogorov-Smirnov test. The differences between the non-parametric quantitative variables were evaluated with the Mann-Whitney U statistical test and the qualitative variables were evaluated using with the χ2 test or Fisher's exact test. Spearman's correlation was used to evaluate the correlation between variables and a significative staging of depression and anxiety. A binary logistic regression was done to identify the association between the variables and the significative staging of depression and anxiety using the variables that previously had a correlation with a P-value < .01. Statistical analysis was conducted in IBM-Statistical Package for Social Sciences version 23 (IBM Corp., USA)25 , and the figure was produced using R version 4.0.2 (R Core Team, Austria)26 with the package ggplot2 version 3.3.2 (Wickham, USA).27
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3

Anxiety and Depression Assessment Protocol

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The studied sample was divided into 2 groups to address anxiety and depression, mild and significative symptoms (instead of using the classic grades of none, mild, moderate, moderate-severe, and severe), using a score of 10 as cut point. Continuous variables were represented by mean ± standard deviation and median [interquartile range], and the categorical variables were presented as percentages. To identify the variable distribution type, they were analyzed using the Kolmogorov-Smirnov test. The differences between the non-parametric quantitative variables were evaluated with the Mann-Whitney U statistical test and the qualitative variables were evaluated using with the χ2 test or Fisher's exact test. Spearman's correlation was used to evaluate the correlation between variables and a significative staging of depression and anxiety. A binary logistic regression was done to identify the association between the variables and the significative staging of depression and anxiety using the variables that previously had a correlation with a P-value < .01. Statistical analysis was conducted in IBM-Statistical Package for Social Sciences version 23 (IBM Corp., USA)25 , and the figure was produced using R version 4.0.2 (R Core Team, Austria)26 with the package ggplot2 version 3.3.2 (Wickham, USA).27
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